Novel methods of constructing libraries of genetic packages that collectively display the members of a diverse family of peptides, polypeptides or proteins

ABSTRACT

The present invention relates to constructing libraries of genetic packages that display a member of a diverse family of peptides, polypeptides or proteins and collectively display at least a portion of the diversity of the family. In a preferred embodiment, the displayed polypeptides are human Fabs.  
     More specifically, the invention is directed to the methods of cleaving single-stranded nucleic acids at chosen locations, the cleaved nucleic acids encoding, at least in part, the peptides, polypeptides or proteins displayed on the genetic packages of the libraries of the invention. In a preferred embodiment, the genetic packages are filamentous phage or phagemids.  
     The present invention further relates to methods of screening the libraries of genetic packages that display useful peptides, polypeptides and proteins and to the peptides, polypeptides and proteins identified by such screening.

BACKGROUND OF THE INVENTION

[0001] It is now common practice in the art to prepare libraries of genetic packages that display a member of a diverse family of peptides, polypeptides or proteins and collectively display at least a portion of the diversity of the family. In many common libraries, the displayed peptides, polypeptides or proteins are related to antibodies. Often, they are Fabs or single chain antibodies.

[0002] In general, the DNAs that encode members of the families to be displayed must be amplified before they are cloned and used to display the desired member on the surface of a genetic package. Such amplification typically makes use of forward and backward primers.

[0003] Such primers can be complementary to sequences native to the DNA to be amplified or complementary to oligonucleotides attached at the 5′ or 3′ ends of that DNA. Primers that are complementary to sequences native to the DNA to be amplified are disadvantaged in that they bias the members of the families to be displayed. Only those members that contain a sequence in the native DNA that is substantially complementary to the primer will be amplified. Those that do not will be absent from the family. For those members that are amplified, any diversity within the primer region will be suppressed.

[0004] For example, in European patent 368,684 B1, the primer that is used is at the 5′ end of the V_(H) region of an antibody gene. It anneals to a sequence region in the native DNA that is said to be “sufficiently well conserved” within a single species. Such primer will bias the members amplified to those having this “conserved” region. Any diversity within this region is extinguished.

[0005] It is generally accepted that human antibody genes arise through a process that involves a combinatorial selection of V and J or V, D, and J followed by somatic mutations. Although most diversity occurs in the Complementary Determining Regions (CDRs), diversity also occurs in the more conserved Framework Regions (FRs) and at least some of this diversity confers or enhances specific binding to antigens (Ag). As a consequence, libraries should contain as much of the CDR and FR diversity as possible.

[0006] To clone the amplified DNAs for display on a genetic package of the peptides, polypeptides or proteins that they encode, the DNAs must be cleaved to produce appropriate ends for ligation to a vector. Such cleavage is generally effected using restriction endonuclease recognition sites carried on the primers. When the primers are at the 5′ end of DNA produced from reverse transcription of RNA, such restriction leaves deleterious 5′ untranslated regions in the amplified DNA. These regions interfere with expression of the cloned genes and thus the display of the peptides, polypeptides and proteins coded for by them.

SUMMARY OF THE INVENTION

[0007] It is an object of this invention to provide novel methods for constructing libraries of genetic packages that display a member of a diverse family of peptides, polypeptides or proteins and collectively display at least a portion of the diversity of the family. These methods are not biased toward DNAs that contain native sequences that are complementary to the primers used for amplification. They also enable any sequences that may be deleterious to expression to be removed from the amplified DNA before cloning and displaying.

[0008] It is another object of this invention to provide a method for cleaving single-stranded nucleic acid sequences at a desired location, the method comprising the steps of:

[0009] (i) contacting the nucleic acid with a single-stranded oligonucleotide, the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired and including a sequence that with its complement in the nucleic acid forms a restriction endonuclease recognition site that on restriction results in cleavage of the nucleic acid at the desired location; and

[0010] (ii) cleaving the nucleic acid solely at the recognition site formed by the complementation of the nucleic acid and the oligonucleotide;

[0011] the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.

[0012] It is a further object of this invention to provide an alternative method for cleaving single-stranded nucleic acid sequences at a desired location, the method comprising the steps of:

[0013] (i) contacting the nucleic acid with a partially double-stranded oligonucleotide, the single-stranded region of the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired, and the double-stranded region of the oligonucleotide having a Type II-S restriction endonuclease recognition site, whose cleavage site is located at a known distance from the recognition site; and

[0014] (ii) cleaving the nucleic acid solely at the cleavage site formed by the complementation of the nucleic acid and the single-stranded region of the oligonucleotide;

[0015] the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.

[0016] It is another objective of the present invention to provide a method of capturing DNA molecules that comprise a member of a diverse family of DNAs and collectively comprise at least a portion of the diversity of the family. These DNA molecules in single-stranded form have been cleaved by one of the methods of this invention. This method involves ligating the individual single-stranded DNA members of the family to a partially duplex DNA complex. The method comprises the steps of:

[0017] (i) contacting a single-stranded nucleic acid sequence that has been cleaved with a restriction endonuclease with a partially double-stranded oligonucleotide, the single-stranded region of the oligonucleotide being functionally complementary to the nucleic acid in the region that remains after cleavage, the double-stranded region of the oligonucleotide including any sequences necessary to return the sequences that remain after cleavage into proper reading frame for expression and containing a restriction endonuclease recognition site 5′ of those sequences; and

[0018] (ii) cleaving the partially double-stranded oligonucleotide sequence solely at the restriction endonuclease recognition site contained within the double-stranded region of the partially double-stranded oligonucleotide.

[0019] It is another object of this invention to prepare libraries, that display a diverse family of peptides, polypeptides or proteins and collectively display at least part of the diversity of the family, using the methods and DNAs described above.

[0020] It is an object of this invention to screen those libraries to identify useful peptides, polypeptides and proteins and to use those substances in human therapy.

BRIEF DESCRIPTION OF THE DRAWINGS

[0021]FIG. 1 is a schematic of various methods that may be employed to amplify VH genes without using primers specific for VH sequences.

[0022]FIG. 2 is a schematic of various methods that may be employed to amplify VL genes without using VL sequences.

[0023]FIG. 3 depicts gel analysis of cleaved kappa DNA from Example 2.

[0024]FIG. 4 depicts gel analysis of cleaved kappa DNA from Example 2.

[0025]FIG. 5 depicts gel analysis of amplified kappa DNA from Example 2.

[0026]FIG. 6 depicts gel purified amplified kappa DNA from Example 2.

TERMS

[0027] In this application, the following terms and abbreviations are used: Sense strand The upper strand of ds DNA as usually written. In the sense strand, 5′-ATG-3′ codes for Met. Antisense strand The lower strand of ds DNA as usually written. In the antisense strand, 3′-TAC-5′ would correspond to a Met codon in the sense strand. Forward primer: A “forward” primer is complementary to a part of the sense strand and primes for synthesis of a new antisense- strand molecule. “Forward primer” and “lower-strand primer” are equivalent. Backward primer: A “backward” primer is complementary to a part of the antisense strand and primes for synthesis of a new sense- strand molecule. “Backward primer” and “top-strand primer” are equivalent. Bases: Bases are specified either by their position in a vector or gene as their position within a gene by codon and base. For example, “89.1” is the first base of codon 89, 89.2 is the second base of codon 89. Sv Streptavidin Ap Ampicillin ap^(R) A gene conferring ampicillin resistance. RE Restriction endonuclease URE Universal restriction endonuclease Functionally Two sequences are sufficiently complementary complementary so as to anneal under the chosen conditions. RERS Restriction endonuclease recognition site AA Amino acid PCR Polymerization chain reaction GLGs Germline genes Ab Antibody: an immunoglobin. The term also covers any protein having a binding domain which is homologous to an immunoglobin binding domain. A few examples of antibodies within this definition are, inter alia, immunoglobin isotypes and the Fab, F(ab¹)₂, scfv, Fv, dAb and Fd fragments. Fab Two chain molecule comprising an Ab light chain and part of a heavy-chain. scFv A single-chain Ab comprising either VH::linker::VL or VL::linker::VH w.t. Wild type HC Heavy chain LC Light chain VK A variable domain of a Kappa light chain. VH A variable domain of a heavy chain. VL A variable domain of a lambda light chain.

[0028] In this application, all references referred to are specifically incorporated by reference.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0029] The nucleic acid sequences that are useful in the methods of this invention, i.e., those that encode at least in part the individual peptides, polypeptides and proteins displayed on the genetic packages of this invention, may be naturally occurring, synthetic or a combination thereof. They may be mRNA, DNA or cDNA. In the preferred embodiment, the nucleic acids encode antibodies. Most preferably, they encode Fabs.

[0030] The nucleic acids useful in this invention may be naturally diverse, synthetic diversity may be introduced into those naturally diverse members, or the diversity may be entirely synthetic. For example, synthetic diversity can be introduced into one or more CDRs of antibody genes.

[0031] Synthetic diversity may be created, for example, through the use of TRIM technology (U.S. Pat. No. 5,869,644). TRIM technology allows control over exactly which amino-acid types are allowed at variegated positions and in what proportions. In TRIM technology, codons to be diversified are synthesized using mixtures of trinucleotides. This allows any set of amino acid types to be included in any proportion.

[0032] Another alternative that may be used to generate diversified DNA is mixed oligonucleotide synthesis. With TRIM technology, one could allow Ala and Trp. With mixed oligonucleotide synthesis, a mixture that included Ala and Trp would also necessarily include Ser and Gly. The amino-acid types allowed at the variegated positions are picked with reference to the structure of antibodies, or other peptides, polypeptides or proteins of the family, the observed diversity in germline genes, the observed somatic mutations frequently observed, and the desired areas and types of variegation.

[0033] In a preferred embodiment of this invention, the nucleic acid sequences for at least one CDR or other region of the peptides, polypeptides or proteins of the family are cDNAs produced by reverse transcription from mRNA. More preferably, the mRNAs are obtained from peripheral blood cells, bone marrow cells, spleen cells or lymph node cells (such as B-lymphocytes or plasma cells) that express members of naturally diverse sets of related genes. More preferable, the mRNAs encode a diverse family of antibodies. Most preferably, the mRNAs are obtained from patients suffering from at least one autoimmune disorder or cancer. Preferably, mRNAs containing a high diversity of autoimmune diseases, such as systemic lupus erythematosus, systemic sclerosis, rheumatoid arthritis, antiphospholipid syndrome and vasculitis are used.

[0034] In a preferred embodiment of this invention, the cDNAs are produced from the mRNAs using reverse transcription. In this preferred embodiment, the mRNAs are separated from the cell and degraded using standard methods, such that only the full length (i.e., capped) mRNAs remain. The cap is then removed and reverse transcription used to produce the cDNAs.

[0035] The reverse transcription of the first (antisense) strand can be done in any manner with any suitable primer. See, e.g., H J de Haard et al., Journal of Biological Chemistry, 274(26):18218-30 (1999). In the preferred embodiment of this invention where the mRNAs encode antibodies, primers that are complementary to the constant regions of antibody genes may be used. Those primers are useful because they do not generate bias toward subclasses of antibodies. In another embodiment, poly-dT primers may be used (and may be preferred for the heavy-chain genes). Alternatively, sequences complementary to the primer may be attached to the termini of the antisense strand.

[0036] In one preferred embodiment of this invention, the reverse transcriptase primer may be biotinylated, thus allowing the cDNA product to be immobilized on streptavidin (Sv) beads. Immobilization can also be effected using a primer labeled at the 5′ end with one of a) free amine group, b) thiol, c) carboxylic acid, or d) another group not found in DNA that can react to form a strong bond to a known partner on an insoluble medium. If, for example, a free amine (preferably primary amine) is provided at the 5′ end of a DNA primer, this amine can be reacted with carboxylic acid groups on a polymer bead using standard amide-forming chemistry. If such preferred immobilization is used during reverse transcription, the top strand RNA is degraded using well-known enzymes, such as a combination of RNAseH and RNAseA, either before or after immobilization.

[0037] The nucleic acid sequences useful in the methods of this invention are generally amplified before being used to display the peptides, polypeptides or proteins that they encode. Prior to amplification, the single-stranded DNAs may be cleaved using either of the methods described before. Alternatively, the single-stranded DNAs may be amplified and then cleaved using one of those methods.

[0038] Any of the well known methods for amplifying nucleic acid sequences may be used for such amplification. Methods that maximize, and do not bias, diversity are preferred. In a preferred embodiment of this invention where the nucleic acid sequences are derived from antibody genes, the present invention preferably utilizes primers in the constant regions of the heavy and light chain genes and primers to a synthetic sequence that are attached at the 5′ end of the sense strand Priming at such synthetic sequence avoids the use of sequences within the variable regions of the antibody genes. Those variable region priming sites generate bias against V genes that are either of rare subclasses or that have been mutated at the priming sites. This bias is partly due to suppression of diversity within the primer region and partly due to lack of priming when many mutations are present in the region complementary to the primer. The methods disclosed in this invention have the advantage of not biasing the population of amplified antibody genes for particular V gene types.

[0039] The synthetic sequences may be attached to the 5′ end of the DNA strand by various methods well known for ligating DNA sequences together. RT CapExtention is one preferred method.

[0040] In RT CapExtention (derived from Smart PCR^((TM)), a short overlap (5′- . . . GGG-3′ in the upper-strand primer (USP-GGG) complements 3′-CCC . . . 5′ in the lower strand) and reverse transcriptases are used so that the reverse complement of the upper-strand primer is attached to the lower strand.

[0041] In a preferred embodiment of this invention, the upper strand or lower strand primer may be also biotinylated or labeled at the 5′ end with one of a) free amino group, b) thiol, c) carboxylic acid and d) another group not found in DNA that can react to form a strong bond to a known partner as an insoluble medium. These can then be used to immobilize the labeled strand after amplification. The immobilized DNA can be either single or double-stranded.

[0042]FIG. 1 shows a schematic of the amplification of VH genes. FIG. 1, Panel A shows a primer specific to the poly-dT region of the 3′ UTR priming synthesis of the first, lower strand. Primers that bind in the constant region are also suitable. Panel B shows the lower strand extended at its 3′ end by three Cs that are not complementary to the mRNA. Panel C shows the result of annealing a synthetic top-strand primer ending in three GGGs that hybridize to the 3′ terminal CCCs and extending the reverse transcription extending the lower strand by the reverse complement of the synthetic primer sequence. Panel D shows the result of PCR amplification using a 5′ biotinylated synthetic top-strand primer that replicates the 5′ end of the synthetic primer of panel C and a bottom-strand primer complementary to part of the constant domain. Panel E shows immobilized double-stranded (ds) cDNA obtained by using a 5′-biotinylated top-strand primer.

[0043]FIG. 2 shows a similar schematic for amplification of VL genes. FIG. 2, Panel A shows a primer specific to the constant region at or near the 3′ end priming synthesis of the first, lower strand. Primers that bind in the poly-dT region are also suitable. Panel B shows the lower strand extended at its 3′ end by three Cs that are not complementary to the mRNA. Panel C shows the result of annealing a synthetic top-strand primer ending in three GGGs that hybridize to the 3′ terminal CCCs and extending the reverse transcription extending the lower strand by the reverse complement of the synthetic primer sequence. Panel D shows the result of PCR amplification using a 5′ biotinylated synthetic top-strand primer that replicates the 5′ end of the synthetic primer of panel C and a bottom-strand primer complementary to part of the constant domain. The bottom-strand primer also contains a useful restriction endonuclease site, such as AscI. Panel E shows immobilized ds cDNA obtained by using a 5′-biotinylated top-strand primer.

[0044] In FIGS. 1 and 2, each V gene consists of a 5′ untranslated region (UTR) and a secretion signal, followed by the variable region, followed by a constant region, followed by a 3′ untranslated region (which typically ends in poly-A). An initial primer for reverse transcription may be complementary to the constant region or to the poly A segment of the 3′-UTR. For human heavy-chain genes, a primer of 15 T is preferred. Reverse transcriptases attach several C residues to the 3′ end of the newly synthesized DNA. RT CapExtention exploits this feature. The reverse transcription reaction is first run with only a lower-strand primer. After about 1 hour, a primer ending in GGG (USP-GGG) and more RTase are added. This causes the lower-strand cDNA to be extended by the reverse complement of the USP-GGG up to the final GGG. Using one primer identical to part of the attached synthetic sequence and a second primer complementary to a region of known sequence at the 3′ end of the sense strand, all the V genes are amplified irrespective of their V gene subclass.

[0045] After amplification, the DNAs of this invention are rendered single-stranded. For example, the strands can be separated by using a biotinylated primer, capturing the biotinylated product on streptavidin beads, denaturing the DNA, and washing away the complementary strand. Depending on which end of the captured DNA is wanted, one will choose to immobilize either the upper (sense) strand or the lower (antisense) strand.

[0046] To prepare the single-stranded amplified DNAs for cloning into genetic packages so as to effect display of the peptides, polypeptides or proteins encoded, at least in part, by those DNAS, they must be manipulated to provide ends suitable for cloning and expression. In particular, any 5′ untranslated regions and mammalian signal sequences must be removed and replaced, in frame, by a suitable signal sequence that functions in the display host. Additionally, parts of the variable domains (in antibody genes) may be removed and replaced by synthetic segments containing synthetic diversity. The diversity of other gene families may likewise be expanded with synthetic diversity.

[0047] According to the methods of this invention, there are two ways to manipulate the single-stranded amplified DNAs for cloning. The first method comprises the steps of:

[0048] (i) contacting the nucleic acid with a single-stranded oligonucleotide, the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired and including a sequence that with its complement in the nucleic acid forms a restriction endonuclease recognition site that on restriction results in cleavage of the nucleic acid at the desired location; and

[0049] (ii) cleaving the nucleic acid solely at the recognition site formed by the complementation of the nucleic acid and the oligonucleotide;

[0050] the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.

[0051] In this first method, short oligonucleotides are annealed to the single-stranded DNA so that restriction endonuclease recognition sites formed within the now locally double-stranded regions of the DNA can be cleaved. In particular, a recognition site that occurs at the same position in a substantial fraction of the single-stranded DNAs is identical.

[0052] For antibody genes, this can be done using a catalog of germline sequences. See, e.g., “http://www.mrc-cpe.cam.ac.uk/imt-doc/restricted/ok.html.” Updates can be obtained from this site under the heading “Amino acid and nucleotide sequence alignments.” For other families, similar comparisons exist and may be used to select appropriate regions for cleavage and to maintain diversity.

[0053] For example, Table 195 depicts the DNA sequences of the FR3 regions of the 51 known human VH germline genes. In this region, the genes contain restriction endonuclease recognition sites shown in Table 200. Restriction endonucleases that cleave a large fraction of germline genes at the same site are preferred over endonucleases that cut at a variety of sites. Furthermore, it is preferred that there be only one site for the restriction endonucleases within the region to which the short oligonucleotide binds on the single-stranded DNA, e.g., about 10 bases on either side of the restriction endonuclease recognition site.

[0054] An enzyme that cleaves downstream in FR3 is also more preferable because it captures fewer mutations in the framework. This may be advantageous is some cases. However, it is well known that framework mutations exist and confer and enhance antibody binding. The present invention, by choice of appropriate restriction site, allows all or part of FR3 diversity to be captured. Hence, the method also allows extensive diversity to be captured.

[0055] Finally, in the methods of this invention restriction endonucleases that are active between about 45° and about 75° C. are used. Preferably enzymes that are active above 50° C., and more preferably active about 55° C., are used. Such temperatures maintain the nucleic acid sequence to be cleaved in substantially single-stranded form.

[0056] Enzymes shown in Table 200 that cut many of the heavy chain FR3 germline genes at a single position include: MaeIII(24@4), Tsp45I(21@4), HphI(44@5), BsaJT(23@65), AluI(23@47), BlpI(21@48), DdeI(29@58), BglTI(10@61), MslI(44@72), BsiEI(23@74), EaeI(23@74), EagI(23@74), HaeIII(25@75), Bst4CI(51@86), HpyCH41II(51@86), HinfI(38@2), MlyI(18@2), PleI(18@2), MnlI(31@67), HpyCH4V(21@44), BsmAI(16@11), BpmI(19@12), XmnI(12@30), and SacI(11@51). (The notation used means, for example, that BsmAI cuts 16 of the FR3 germline genes with a restriction endonuclease recognition site beginning at base 11 of FR3.)

[0057] For cleavage of human heavy chains in FR3, the preferred restriction endonucleases are: Bst4CI (or TaaI or HpyCH41II), BlpI, HpyCH4V, and MslI. Because ACNGT (the restriction endonuclease recognition site for Bst4CI, TaaI, and HpyCH41II) is found at a consistent site in all the human FR3 germline genes, one of those enzymes is the most preferred for capture of heavy chain CDR3 diversity. BlpI and HpyCH4V are complementary. BlpI cuts most members of the VH1 and VH4 families while HpyCH4V cuts most members of the VH3, VH5, VH6, and VH7 families. Neither enzyme cuts VH2s, but this is a very small family, containing only three members. Thus, these enzymes may also be used in preferred embodiments of the methods of this invention.

[0058] The restriction endonucleases HpyCH4III, Bst4CI, and TaaI all recognize 5′-ACnGT-3′ and cut upper strand DNA after n and lower strand DNA before the base complementary to n. This is the most preferred restriction endonuclease recognition site for this method on human heavy chains because it is found in all germline genes. Furthermore, the restriction endonuclease recognition region (ACnGT) matches the second and third bases of a tyrosine codon (tay) and the following cysteine codon (tgy) as shown in Table 206. These codons are highly conserved, especially the cysteine in mature antibody genes.

[0059] Table 250 E shows the distinct oligonucleotides of length 22 (except the last one which is of length 20) bases. Table 255 C shows the analysis of 1617 actual heavy chain antibody genes. Of these, 1511 have the site and match one of the candidate oligonucleotides to within 4 mismatches. Eight oligonucleotides account for most of the matches and are given in Table 250 F.1. The 8 oligonucleotides are very similar so that it is likely that satisfactory cleavage will be achieved with only one oligonucleotide (such as H43.77.97.1-02#1) by adjusting temperature, pH, salinity, and the like. One or two oligonucleotides may likewise suffice whenever the germline gene sequences differ very little and especially if they differ very little close to the restriction endonuclease recognition region to be cleaved. Table 255 D shows a repeat analysis of 1617 actual heavy chain antibody genes using only the 8 chosen oligonucleotides. This shows that 1463 of the sequences match at least one of the oligonucleotides to within 4 mismatches and have the site as expected. Only 7 sequences have a second HpyCH4III restriction endonuclease recognition region in this region.

[0060] Another illustration of choosing an appropriate restriction endonuclease recognition site involves cleavage in FR1 of human heavy chains. Cleavage in FR1 allows capture of the entire CDR diversity of the heavy chain.

[0061] The germline genes for human heavy chain FR1 are shown in Table 217. Table 220 shows the restriction endonuclease recognition sites found in human germline genes FR1s. The preferred sites are BsgI(GTGCAG;39@4), BsoFI(GCngc;43@6,11@9,2@3,1@12), TseI (Gcwgc;43@6,11@9,2@3,1@12), MspA1I(CMGckg;46@7,2@1), PvuII(CAGctg;46@7,2@1), AluI(AGct;48@82@2), DdeI (Ctnag;22@52,9@48), HphI(tcacc;22@80), BssKI(Nccngg;35@39,2@40), BsaJI(Ccnngg;32@40,2@41), BstNI(CCwgg;33@40), ScrFI (CCngg;35@40,2@41), EcoO109I(RGgnccy;22@46, 11@43), Sau96I(Ggncc;23@47,11@44), AvaII(Ggwcc;23@47,4@44), PpuMI(RGgwccy;22@46,4@43), BsmFI(gtccc;20@48), HinfI(Gantc;34@16,21@56,21@77), TfiT(21@77), MlyI(GAGTC;34@16), MlyI(gactc;21@56), and AlwNI(CAGnnnctg;22@68). The more preferred sites are MspAI and PvuII. MspAI and PvuII have 46 sites at 7-12 and 2 at 1-6. To avoid cleavage at both sites, oligonucleotides are used that do not fully cover the site at 1-6. Thus, the DNA will not be cleaved at that site. We have shown that DNA that extends 3, 4, or 5 bases beyond a PvuII-site can be cleaved efficiently.

[0062] Another illustration of choosing an appropriate restriction endonuclease recognition site involves cleavage in FR1 of human kappa light chains. Table 300 shows the human kappa FR1 germline genes and Table 302 shows restriction endonuclease recognition sites that are found in a substantial number of human kappa FR1 germline genes at consistent locations. Of the restriction endonuclease recognition sites listed, BsmAI and PflFI are the most preferred enzymes. BsmAI sites are found at base 18 in 35 of 40 germline genes. PflFI sites are found in 35 of 40 germline genes at base 12.

[0063] Another example of choosing an appropriate restriction endonuclease recognition site involves cleavage in FR1 of the human lambda light chain. Table 400 shows the 31 known human lambda FR1 germline gene sequences. Table 405 shows restriction endonuclease recognition sites found in human lambda FR1 germline genes. HinfI and DdeI are the most preferred restriction endonucleases for cutting human lambda chains in FR1.

[0064] After the appropriate site or sites for cleavage are chosen, one or more short oligonucleotides are prepared so as to functionally complement, alone or in combination, the chosen recognition site. The oligonucleotides also include sequences that flank the recognition site in the majority of the amplified genes. This flanking region allows the sequence to anneal to the single-stranded DNA sufficiently to allow cleavage by the restriction endonuclease specific for the site chosen.

[0065] The actual length and sequence of the oligonucleotide depends on the recognition site and the conditions to be used for contacting and cleavage. The length must be sufficient so that the oligonucleotide is functionally complementary to the single-stranded DNA over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and solely at the desired location.

[0066] Typically, the oligonucleotides of this preferred method of the invention are about 17 to about 30 nucleotides in length. Below about 17 bases, annealing is too weak and above 30 bases there can be a loss of specificity. A preferred length is 18 to 24 bases.

[0067] Oligonucleotides of this length need not be identical complements of the germline genes. Rather, a few mismatches taken may be tolerated. Preferably, however, no more than 1-3 mismatches are allowed. Such mismatches do not adversely affect annealing of the oligonucleotide to the single-stranded DNA. Hence, the two DNAs are said to be functionally complementary.

[0068] The second method to manipulate the amplified single-stranded DNAs of this invention for cloning comprises the steps of:

[0069] (i) contacting the nucleic acid with a partially double-stranded oligonucleotide, the single-stranded region of the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired, and the double-stranded region of the oligonucleotide having a Type II-S restriction endonuclease recognition site, whose cleavage site is located at a known distance from the recognition site; and

[0070] (ii) cleaving the nucleic acid solely at the cleavage site formed by the complementation of the nucleic acid and the single-stranded region of the oligonucleotide;

[0071] the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.

[0072] This second method employs Universal Restriction Endonucleases (“URE”). UREs are partially double-stranded oligonucleotides. The single-stranded portion or overlap of the URE consists of a DNA adapter that is functionally complementary to the sequence to be cleaved in the single-stranded DNA. The double-stranded portion consists of a type II-S restriction endonuclease recognition site.

[0073] The URE method of this invention is specific and precise and can tolerate some (e.g., 1-3) mismatches in the complementary regions, i.e., it is functionally complementary to that region. Further, conditions under which the URE is used can be adjusted so that most of the genes that are amplified can be cut, reducing bias in the library produced from those genes.

[0074] The sequence of the single-stranded DNA adapter or overlap portion of the URE typically consists of about 14-22 bases. However, longer or shorter adapters may be used. The size depends on the ability of the adapter to associate with its functional complement in the single-stranded DNA and the temperature used for contacting the URE and the single-stranded DNA at the temperature used for cleaving the DNA with the type II-S enzyme. The adapter must be functionally complementary to the single-stranded DNA ver a large enough region to allow the two strands to associate such that the cleavage may occur at the chosen temperature and at the desired location. We prefer singe-stranded or overlap portions of 14-17 bases in length, and more preferably 18-20 bases in length.

[0075] The site chosen for cleavage using the URE is preferably one that is substantially conserved in the family of amplified DNAs. As compared to the first cleavage method of this invention, these sites do not need to be endonuclease recognition sites. However, like the first method, the sites chosen can be synthetic rather than existing in the native DNA. Such sites may be chosen by references to the sequences of known antibodies or other families of genes. For example, the sequences of many germline genes are reported at http://www.mrc-cpe.cam.ac.uk/imt-doc/restricted/ok.html. For example, one preferred site occurs near the end of FR3—codon 89 through the second base of codon 93. CDR3 begins at codon 95.

[0076] The sequences of 79 human heavy-chain genes are also available at http://www.ncbi.nlm.nih.gov/entre2/nucleotide.html. This site can be used to identify appropriate sequences for URE cleavage according to the methods of this invention. See, e.g., Table 8B.

[0077] Most preferably, one or more sequences are identified using these sites or other available sequence information. These sequences together are present in a substantial fraction of the amplified DNAs. For example, multiple sequences could be used to allow for known diversity in germline genes or for frequent somatic mutations. Synthetic degenerate sequences could also be used. Preferably, a sequence(s) that occurs in at least 65% of genes examined with no more than 2-3 mismatches is chosen

[0078] URE single-stranded adapters or overlaps are then made to be complementary to the chosen regions. Conditions for using the UREs are determined empirically. These conditions should allow cleavage of DNA that contains the functionally complementary sequences with no more than 2 or 3 mismatches but that do not allow cleavage of DNA lacking such sequences.

[0079] As described above, the double-stranded portion of the URE includes a Type II-S endonuclease recognition site. Any Type II-S enzyme that is active at a temperature necessary to maintain the single-stranded DNA substantially in that form and to allow the single-stranded DNA adapter portion of the URE to anneal long enough to the single-stranded DNA to permit cleavage at the desired site may be used.

[0080] The preferred Type II-S enzymes for use in the URE methods of this invention provide asymmetrical cleavage of the single-stranded DNA. Among these are the enzymes listed in Table 800. The most preferred Type II-S enzyme is FokI.

[0081] When the preferred Fok I containing URE is used, several conditions are preferably used to effect cleavage:

[0082] 1) Excess of the URE over target DNA should be present to activate the enzyme. URE present only in equimolar amounts to the target DNA would yield poor cleavage of ssDNA because the amount of active enzyme available would be limiting.

[0083] 2) An activator may be used to activate part of the FokI enzyme to dimerize without causing cleavage. Examples of appropriate activators are shown in Table 510.

[0084] 3) The cleavage reaction is performed at a temperature between 45°-75° C., preferably above 50° C. and most preferably above 55° C.

[0085] The UREs used in the prior art contained a 14-base single-stranded segment, a 10-base stem (containing a FokI site), followed by the palindrome of the 10-base stem. While such UREs may be used in the methods of this invention, the preferred UREs of this invention also include a segment of three to eight bases (a loop) between the FokI restriction endonuclease recognition site containing segments. In the preferred embodiment, the stem (containing the FokI site) and its palindrome are also longer than 10 bases. Preferably, they are 10-14 bases in length. Examples of these “lollipop” URE adapters are shown in Table 5.

[0086] One example of using a URE to cleave an single-stranded DNA involves the FR3 region of human heavy chain. Table 508 shows an analysis of 840 full-length mature human heavy chains with the URE recognition sequences shown. The vast majority (718/840=0.85) will be recognized with 2 or fewer mismatches using five UREs (VHS881-1.1, VHS881-1.2, VHS881-2.1, VHS881-4.1, and VHS881-9.1). Each has a 20-base adaptor sequence to complement the germline gene, a ten-base stem segment containing a FokI site, a five base loop, and the reverse complement of the first stem segment. Annealing those adapters, alone or in combination, to single-stranded antisense heavy chain DNA and treating with FokI in the presence of, e.g., the activator FOKIact, will lead to cleavage of the antisense strand at the position indicated.

[0087] Another example of using a URE(s) to cleave a single-stranded DNA involves the FR1 region of the human Kappa light chains. Table 512 shows an analysis of 182 full-length human kappa chains for matching by the four 19-base probe sequences shown. Ninety-six percent of the sequences match one of the probes with 2 or fewer mismatches. The URE adapters shown in Table 512 are for cleavage of the sense strand of kappa chains. Thus, the adaptor sequences are the reverse complement of the germline gene sequences. The URE consists of a ten-base stem, a five base loop, the reverse complement of the stem and the complementation sequence. The loop shown here is TTGTT, but other sequences could be used. Its function is to interrupt the palindrome of the stems so that formation of a lollypop monomer is favored over dimerization. Table 512 also shows where the sense strand is cleaved.

[0088] Another example of using a URE to cleave a single-stranded DNA involves the human lambda light chain. Table 515 shows analysis of 128 human lambda light chains for matching the four 19-base probes shown. With three or fewer mismatches, 88 of 128 (69%) of the chains match one of the probes. Table 515 also shows URE adapters corresponding to these probes. Annealing these adapters to upper-strand ssDNA of lambda chains and treatment with FokI in the presence of FOKIact at a temperature at or above 45° C. will lead to specific and precise cleavage of the chains.

[0089] The conditions under which the short oligonucleotide sequences of the first method and the UREs of the second method are contacted with the single-stranded DNAs may be empirically determined. The conditions must be such that the single-stranded DNA remains in substantially single-stranded form. More particularly, the conditions must be such that the single-stranded DNA does not form loops that may interfere with its association with the oligonucleotide sequence or the URE or that may themselves provide sites for cleavage by the chosen restriction endonuclease.

[0090] The effectiveness and specificity of short oligonucleotides (first method) and UREs (second method) can be adjusted by controlling the concentrations of the URE adapters/oligonucleotides and substrate DNA, the temperature, the pH, the concentration of metal ions, the ionic strength, the concentration of chaotropes (such as urea and formamide), the concentration of the restriction endonuclease(e.g., FokI), and the time of the digestion. These conditions can be optimized with synthetic oligonucleotides having: 1) target germline gene sequences, 2) mutated target gene sequences, or 3) somewhat related non-target sequences. The goal is to cleave most of the target sequences and minimal amounts of non-targets.

[0091] In the preferred embodiment of this invention, the single-stranded DNA is maintained in substantially that form using a temperature between 45° C. to 75° C. More preferably, a temperature between 50° C. and 60° C., most preferably between 55° C. and 60° C., is used. These temperatures are employed both when contacting the DNA with the oligonucleotide or URE and when cleaving the DNA using the methods of this invention.

[0092] The two cleavage methods of this invention have several advantages. The first method allows the individual members of the family of single-stranded DNAs to be cleaved solely at one substantially conserved endonuclease recognition site. The method also does not require an endonuclease recognition site to be built in to the reverse transcription or amplification primers. Any native or synthetic site in the family can be used.

[0093] The second method has both of these advantages. In addition, the URE method allows the single-stranded DNAs to be cleaved at positions where no endonuclease recognition site naturally occurs or has been synthetically constructed.

[0094] Most importantly, both cleavage methods permit the use of 5′ and 3′ primers so as to maximize diversity and then cleavage to remove unwanted or deleterious sequences before cloning and display.

[0095] After cleavage of the amplified DNAs using one of the methods of this invention, the DNA is prepared for cloning. This is done by using a partially duplexed synthetic DNA adapter, whose terminal sequence is based on the specific cleavage site at which the amplified DNA has been cleaved.

[0096] The synthetic DNA is designed such that when it is ligated to the cleaved single-stranded DNA, it allows that DNA to be expressed in the correct reading frame so as to display the desired peptide, polypeptide or protein on the surface of the genetic package. Preferably, the double-stranded portion of the adapter comprises the sequence of several codons that encode the amino acid sequence characteristic of the family of peptides, polypeptides or proteins up to the cleavage site. For human heavy chains, the amino acids of the 3-23 framework are preferably used to provide the sequences required for expression of the cleaved DNA.

[0097] Preferably, the double-stranded portion of the adapter is about 12 to 100 bases in length. More preferably, about 20 to 100 bases are used. The double-standard region of the adapter also preferably contains at least one endonuclease recognition site useful for cloning the DNA into a suitable display vector (or a recipient vector used to archive the diversity). This endonuclease restriction site may be native to the germline gene sequences used to extend the DNA sequence. It may be also constructed using degenerate sequences to the native germline gene sequences. Or, it may be wholly synthetic.

[0098] The single-stranded portion of the adapter is complementary to the region of the cleavage in the single-stranded DNA. The overlap can be from about 2 bases up to about 15 bases. The longer the overlap, the more efficient the ligation is likely to be. A preferred length for the overlap is 7 to 10. This allows some mismatches in the region so that diversity in this region may be captured.

[0099] The single-stranded region or overlap of the partially duplexed adapter is advantageous because it allows DNA cleaved at the chosen site, but not other fragments to be captured. Such fragments would contaminate the library with genes encoding sequences that will not fold into proper antibodies and are likely to be non-specifically sticky.

[0100] One illustration of the use of a partially duplexed adaptor in the methods of this invention involves ligating such adaptor to a human FR3 region that has been cleaved, as described above, at 5′-ACnGT-3′ using HpyCH4III, Bst4CI or TaaI.

[0101] Table 250 F.2 shows the bottom strand of the double-stranded portion of the adaptor for ligation to the cleaved bottom-strand DNA. Since the HpyCH4III-Site is so far to the right (as shown in Table 206), a sequence that includes the AflII-site as well as the XbaI site can be added. This bottom strand portion of the partially-duplexed adaptor, H43.XAExt, incorporates both XbaI and AflII-sites. The top strand of the double-stranded portion of the adaptor has neither site (due to planned mismatches in the segments opposite the XbaI and AflII-Sites of H43.XAExt), but will anneal very tightly to H43.XAExt. H43AExt contains only the AflII-site and is to be used with the top strands H43.ABr1 and H43.ABr2 (which have intentional alterations to destroy the AflII-site).

[0102] After ligation, the desired, captured DNA can be PCR amplified again, if desired, using in the preferred embodiment a primer to the downstream constant region of the antibody gene and a primer to part of the double-standard region of the adapter. The primers may also carry restriction endonuclease sites for use in cloning the amplified DNA.

[0103] After ligation, and perhaps amplification, of the partially double-stranded adapter to the single-stranded amplified DNA, the composite DNA is cleaved at chosen 5′ and 3′ endonuclease recognition sites.

[0104] The cleavage sites useful for cloning depend on the phage or phagemid into which the cassette will be inserted and the available sites in the antibody genes. Table 1 provides restriction endonuclease data for 75 human light chains. Table 2 shows corresponding data for 79 human heavy chains in each Table, the endonucleases are ordered by increasing frequency of cutting. In these Tables, Nch is the number of chains cut by the enzyme and Ns is the number of sites (some chains have more than one site).

[0105] From this analysis, SfiI, NotI, AflII, ApaLI, and AscI are very suitable. SfiI and NotI are preferably used in pCES1 to insert the heavy-chain display segment. ApaLI and AscI are preferably used in pCES1 to insert the light-chain display segment.

[0106] BstEII-sites occur in 97% of germ-line JH genes. In rearranged V genes, only 54/79 (68%) of heavy-chain genes contain a BstEII-Site and 7/61 of these contain two sites. Thus, 47/79 (59%) contain a single BstEII-Site. An alternative to using BstEII is to cleave via UREs at the end of JH and ligate to a synthetic oligonucleotide that encodes part of CH1.

[0107] One example of preparing a family of DNA sequences using the methods of this invention involves capturing human CDR 3 diversity. As described above, mRNAs from various autoimmune patients is reverse transcribed into lower strand cDNA. After the top strand RNA is degraded, the lower strand is immobilized and a short oligonucleotide used to cleave the cDNA upstream of CDR3. A partially duplexed synthetic DNA adapter is then annealed to the DNA and the DNA is amplified using a primer to the adapter and a primer to the constant region (after FR4). The DNA is then cleaved using BstEII (in FR4) and a restriction endonuclease appropriate to the partially double-stranded adapter (e.g., Xba I and AflII (in FR3)). The DNA is then ligated into a synthetic VH skeleton such as 3-23.

[0108] One example of preparing a single-stranded DNA that was cleaved using the URE method involves the human Kappa chain. The cleavage site in the sense strand of this chain is depicted in Table 512. The oligonucleotide kapextURE is annealed to the oligonucleotides (kaBR01UR, kaBR02UR, kaBR03UR, and kaBR04UR) to form a partially duplex DNA. This DNA is then ligated to the cleaved soluble kappa chains. The ligation product is then amplified using primers kapextUREPCR and CKForeAsc (which inserts a AscI site after the end of C kappa). This product is then cleaved with ApaLI and AscI and ligated to similarly cut recipient vector.

[0109] Another example involves the cleavage illustrated in Table 515. After cleavage, an extender (ON_LamEx133) and four bridge oligonucleotides (ON_LamB1-133, ON_LamB2-133, ON_LamB3-133, and ON_LamB4-133) are annealed to form a partially duplex DNA. That DNA is ligated to the cleaved lambda-chain sense strands. After ligation, the DNA is amplified with ON_Lam133PCR and a forward primer specific to the lambda constant domain, such as CL2ForeAsc or CL7ForeAsc (Table 130).

[0110] In human heavy chains, one can cleave almost all genes in FR4 (downstream, i.e. toward the 3′ end of the sense strand, of CDR3) at a BstEII-Site that occurs at a constant position in a very large fraction of human heavy-chain V genes. One then needs a site in FR3, if only CDR3 diversity is to be captured, in FR2, if CDR2 and CDR3 diversity is wanted, or in FR1, if all the CDR diversity is wanted. These sites are preferably inserted as part of the partially double-stranded adaptor.

[0111] The preferred process of this invention is to provide recipient vectors having sites that allow cloning of either light or heavy chains. Such vectors are well known and widely used in the art. A preferred phage display vector in accordance with this invention is phage MALIA3. This displays in gene III. The sequence of the phage MALIA3 is shown in Table 120A (annotated) and Table 120B (condensed).

[0112] The DNA encoding the selected regions of the light or heavy chains can be transferred to the vectors using endonucleases that cut either light or heavy chains only very rarely. For example, light chains may be captured with ApaLI and AscI. Heavy-chain genes are preferably cloned into a recipient vector having SfiI, NcoI, XbaI, AflII, BstEII, ApaI, and NotI sites. The light chains are preferably moved into the library as ApaLI-AscI fragments. The heavy chains are preferably moved into the library as SfiI-NotI fragments.

[0113] Most preferably, the display is had on the surface of a derivative of M13 phage. The most preferred vector contains all the genes of M13, an antibiotic resistance gene, and the display cassette. The preferred vector is provided with restriction sites that allow introduction and excision of members of the diverse family of genes, as cassettes. The preferred vector is stable against rearrangement under the growth conditions used to amplify phage.

[0114] In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed in a phagemid vector (e.g., pCES1) that displays the peptide, polypeptide or protein on the III protein. Such vectors may also be used to store the diversity for subsequent display using other vectors or phage.

[0115] In another embodiment, the mode of display may be through a short linker to three possible anchor domains. One anchor domain being the final portion of M13 III (“IIIstump”), a second anchor being the full length III mature protein, and the third being the M13 VIII mature protein.

[0116] The IIIstump fragment contains enough of M13 III to assemble into phage but not the domains involved in mediating infectivity. Because the w.t. III and VIII proteins are present, the phage is unlikely to delete the antibody genes and phage that do delete these segments receive only a very small growth advantage. For each of the anchor domains, the DNA encodes the w.t. AA sequence, but differs from the w.t. DNA sequence to a very high extent. This will greatly reduce the potential for homologous recombination between the display anchor and the w.t. gene that is also present.

[0117] Most preferably, the present invention uses a complete phage carrying an antibiotic-resistance gene (such as an ampicillin-resistance gene) and the display cassette. Because the w.t. iii and viii genes are present, the w.t. proteins are also present. The display cassette is transcribed from a regulatable promoter (e.g., P_(LacZ)) Use of a regulatable promoter allows control of the ratio of the fusion display gene to the corresponding w.t. coat protein. This ratio determines the average number of copies of the display fusion per phage (or phagemid) particle.

[0118] Another aspect of the invention is a method of displaying peptides, polypeptides or proteins (and particularly Fabs) on filamentous phage. In the most preferred embodiment this method displays FABs and comprises:

[0119] a) obtaining a cassette capturing a diversity of segments of DNA encoding the elements:

[0120] P_(req)::RBS1::SS1::VL::CL::stop::RBS2::SS2::VH::CH1::linker::anchor::stop::,

[0121] where P_(req) is a regulatable promoter, RBS1 is a first ribosome binding site, SS1 is a signal sequence operable in the host strain, VL is a member of a diverse set of light-chain variable regions, CL is a light-chain constant region, stop is one or more stop codons, RBS2 is a second ribosome binding site, SS2 is a second signal sequence operable in the host strain, VH is a member of a diverse set of heavy-chain variable regions, CH1 is an antibody heavy-chain first constant domain, linker is a sequence of amino acids of one to about 50 residues, anchor is a protein that will assemble into the filamentous phage particle and stop is a second example of one or more stop codons; and

[0122] b) positioning that cassette within the phage genome to maximize the viability of the phage and to minimize the potential for deletion of the cassette or parts thereof.

[0123] The DNA encoding the anchor protein in the above preferred cassette should be designed to encode the same (or a closely related) amino acid sequence as is found in one of the coat proteins of the phage, but with a distinct DNA sequence. This is to prevent unwanted homologous recombination with the w.t. gene. In addition, the cassette should be placed in the intergenic region. The positioning and orientation of the display cassette can influence the behavior of the phage.

[0124] In one embodiment of the invention, a transcription terminator may be placed after the second stop of the display cassette above (e.g., Trp). This will reduce interaction between the display cassette and other genes in the phage antibody display vector (PADV).

[0125] In another embodiment of the methods of this invention, the phage or phagemid can display proteins other than Fab, by replacing the Fab portions indicated above, with other protein genes.

[0126] Various hosts can be used for growth of the display phage or phagemids of this invention. Such hosts are well known in the art. In the preferred embodiment, where Fabs are being displayed, the preferred host should grow at 30° C. and be RecA⁻ (to reduce unwanted genetic recombination) and EndA⁻ (to make recovery of RF DNA easier). It is also preferred that the host strain be easily transformed by electroporation.

[0127] XL1-Blue MRF′ satisfies most of these preferences, but does not grow well at 30° C. XL1-Blue MRF′ does grow slowly at 38° C. and thus is an acceptable host. TG-1 is also an acceptable host although it is RecA⁺ and EndA⁺. XL1-Blue MRF′ is more preferred for the intermediate host used to accumulate diversity prior to final construction of the library.

[0128] After display, the libraries of this invention may be screened using well known and conventionally used techniques. The selected peptides, polypeptides or proteins may then be used to treat disease. Generally, the peptides, polypeptides or proteins for use in therapy or in pharmaceutical compositions are produced by isolating the DNA encoding the desired peptide, polypeptide or protein from the member of the library selected. That DNA is then used in conventional methods to produce the peptide, polypeptides or protein it encodes in appropriate host cells, preferably mammalian host cells, e.g., CHO cells. After isolation, the peptide, polypeptide or protein is used alone or with pharmaceutically acceptable compositions in therapy to treat disease.

EXAMPLES Example 1 Capturing Kappa Chains with BsmAI

[0129] A repertoire of human-kappa chain mRNAs was prepared by treating total or poly(A+) RNA isolated from a collection of patients having various autoimmune diseases with calf intestinal phosphatase to remove the 5′-phosphate from all molecules that have them, such as ribosomal RNA, fragmented mRNA, tRNA and genomic DNA. Full length mRNA (containing a protective 7-methyl cap structure) is unaffected. The RNA is then treated with tobacco acid pyrophosphatase to remove the cap structure from full length mRNAs leaving a 5′-monophosphate group.

[0130] Full length mRNA's were modified with an adaptor at the 5′ end and then reversed transcribed and amplified using the GeneRACE™ method and kit (Invitrogen). A 5′ biotinylated primer complementary to the adaptor and a 3′ primer complementary to a portion of the construct region were used.

[0131] Approximately 2 micrograms (ug) of human kappa-chain (Igkappa) gene RACE material with biotin attached to 5′-end of upper strand was immobilized on 200 microliters (μL) of Seradyn magnetic beads. The lower strand was removed by washing the DNA with 2 aliquots 200 μL of 0.1 M NaOH (pH 13) for 3 minutes for the first aliquot followed by 30 seconds for the second aliquot. The beads were neutralized with 200 μL of 10 mM Tris (pH 7.5) 100 mM NaCl. The short oligonucleotides shown in Table 525 were added in 40 fold molar excess in 100 μL of NEB buffer 2 (50 μM NaCl, 10 mM Tris-HCl, 10 mM MgCl₂, 1 mM dithiothreitol pH 7.9) to the dry beads. The mixture was incubated at 95° C. for 5 minutes then cooled down to 55° C. over 30 minutes. Excess oligonucleotide was washed away with 2 washes of NEB buffer 3 (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl₂, 1 mM dithiothreitol pH 7.9). Ten units of BsmAI (NEB) were added in NEB buffer 3 and incubated for 1 h at 55° C. The cleaved downstream DNA was collected and purified over a Qiagen PCR purification column (FIGS. 3 and 4).

[0132] A partially double-stranded adaptor was prepared using the oligonucleotide shown in Table 525. The adaptor was added to the single-stranded DNA in 100 fold molar excess along with 1000 units of T4 DNA ligase (NEB) and incubated overnight at 16° C. The excess oligonucleotide was removed with a Qiagen PCR purification column. The ligated material was amplified by PCR using the primers kapPCRt1 and kapfor shown in Table 525 for 10 cycles with the program shown in Table 530.

[0133] The soluble PCR product was run on a gel and showed a band of approximately 700 n, as expected (FIGS. 5 and 6). The DNA was cleaved with enzymes ApaLI and AscI, gel purified, and ligated to similarly cleaved vector pCES1. The presence of the correct size insert was checked by PCR in several clones as shown in FIG. 15.

[0134] Table 500 shows the DNA sequence of a kappa light chain captured by this procedure. Table 501 shows a second sequence captured by this procedure.

[0135] The closest bridge sequence was complementary to the sequence 5′-agccacc-3′, but the sequence captured reads 5′-Tgccacc-3′, showing that some mismatch in the overlapped region is tolerated.

Example 2 Construction of Synthetic CDR1 and CDR2 Diversity in V-3-23 VH Framework

[0136] A synthetic Complementary Determinant Region (CDR) 1 and 2 diversity was constructed in the 3-23 VH framework in a two step process: first, a vector containing the 3-23 VH framework was constructed, and then, a synthetic CDR 1 and 2 was assembled and cloned into this vector.

[0137] For construction of the V3-23 framework, 8 oligos and two PCR primers (long oligonucleotides: TOPFRLA, BOTFR1B, BOTFR2, BOTFR3, F06, BOTFR4, ON-vgC1, and ON-vgC2 and primers: SFPRMET and BOTPCRPRIM, shown in Table 600) that overlap were designed based on the Genebank sequence of V323 VH. The design incorporated at least one useful restriction site in each framework region, as shown in Table 600. In Table 600, the segments that were synthesized are shown as bold, the overlapping regions are underscored, and the PCR priming regions at each end are underscored. A mixture of these 8 oligos was combined at a final concentration of 2.5 uM in a 20 ul Polymerase Chain Reaction (PCR) reaction. The PCR mixture contained 200 uM dNTPs, 2.5 mM MgCl₂, 0.02U Pfu TurboT DNA Polymerase, 1U Qiagen HotStart Taq DNA Polymerase, and 1×Qiagen PCR buffer. The PCR program consisted of 10 cycles of 94° C. for 30s, 55° C. for 30s, and 72° C. for 30s. The assembled V3-23 DNA sequence was then amplified, using 2.5 ul of a 10-fold dilution from the initial PCR in 100 ul PCR reaction. The PCR reaction contained 200 uM dNTPs, 2.5 mM MgCl₂, 0.02U Pfu Turbo™ DNA Polymerase, 1U Qiagen HotStart Taq DNA Polymerase, 1×Qiagen PCR Buffer and 2 outside primers (SFPRMET and BOTPCRPRIM) at a concentration of 1 uM. The PCR program consisted of 23 cycles at 94° C. for 30 s, 55° C. for 30 s, and 72° C. for 60 s. The V3-23 VH DNA sequence was digested and cloned into pCES1 (phagemid vector) using the SfiI and BstEII restriction endonuclease sites (All restriction enzymes mentioned herein were supplied by New England BioLabs, Beverly, Mass. and used as per manufacturer's instructions).

[0138] Stuffer sequences (shown in Table 610 and Table 620) were introduced into pCES1 to replace CDR1/CDR2 sequences (900 bases between BspEI and XbaI RE sites) and CDR3 sequences (358 bases between AflII and BstEII), prior to cloning the CDR1/CDR2 diversity. The new vector is pCES5 and its sequence is given in Table 620. Having stuffers in place of the CDRs avoids the risk that a parental sequence would be over-represented in the library. The CDR1-2 stuffer contains restriction sites for BglII, Bsu36I, BclI, XcmI, MluI, PvuII, HpaI, and HincII, the underscored sites being unique within the vector pCES5. The stuffer that replaces CDR3 contains the unique restriction endonuclease site RsrII. The stuffer sequences are fragments from the penicillase gene of E. coli.

[0139] For the construction of the CDR1 and CDR2 diversity, 4 overlapping oligonucleotides (ON-vgCl, ON_Br12, ON_CD2Xba, and ON-vgC2, shown in Table 600 and Table 630) encoding CDR1/2, plus flanking regions, were designed. A mix of these 4 oligos was combined at a final concentration of 2.5 uM in a 40 ul PCR reaction. Two of the 4 oligos contained variegated sequences positioned at the CDR1 and the CDR2. The PCR mixture contained 200 uM dNTPs, 2.5U Pwo DNA Polymerase (Roche), and 1×Pwo PCR buffer with 2 mM MgSO₄. The PCR program consisted of 10 cycles at 94° C. for 30 s, 60° C. for 30 s, and 72° C. for 60 s. This assembled CDR1/2 DNA sequence was amplified, using 2.5 ul of the mixture in 100 ul PCR reaction. The PCR reaction contained 200 uM dNTPs, 2.5U Pwo DNA Polymerase, 1×Pwo PCR Buffer with 2 mM MgSO₄ and 2 outside primers at a concentration of 1 uM. The PCR program consisted of 10 cycles at 94° C. for 30 s, 60° C. for 30 s, and 72° C. for 60 s. These variegated sequences were digested and cloned into the V3-23 framework in place of the CDR1/2 stuffer.

[0140] We obtained approximately 7×10⁷ independent transformants. Into this diversity, we can clone CDR3 diversity either from donor populations or from synthetic DNA.

[0141] It will be understood that the foregoing is only illustrative of the principles of this invention and that various modifications can be made by those skilled in the art without departing from the scope of and sprit of the invention. TABLE 1 Cleavage of 75 human light chains. Planned location Enzyme Recognition* Nch Ns of site AfeI AGCgct 0 0 AflII Cttaag 0 0 HC FR3 AgeI Accggt 0 0 AscI GGcgcgcc 0 0 After LC BglII Agatct 0 0 BsiWI Cgtacg 0 0 BSpDI ATcgat 0 0 BssHII Gcgcgc 0 0 BstBI TTcgaa 0 0 DraIII CACNNNgtg 0 0 EagI Cggccg 0 0 FseI GGCCGGcc 0 0 FspI TGCgca 0 0 HpaI GTTaac 0 0 MfeI Caattg 0 0 HC FR1 MluI Acgcgt 0 0 NcoI Ccatgg 0 0 Heavy chain signal NheI Gctagc 0 0 HC/anchor linker NotI GCggccgc 0 0 In linker after HC NruI TCGcga 0 0 PacI TTAATtaa 0 0 PmeI GTTTaaac 0 0 PmlI CACgtg 0 0 PvuI CGATcg 0 0 SacII CCGCgg 0 0 SalI Gtcgac 0 0 SfiI GGCCNNNNnggcc 0 0 Heavy Chain signal SgfI GCGATcgc 0 0 SnaBI TACgta 0 0 StuI AGGcct 0 0 XbaI Tctaga 0 0 HC FR3 AatII GACGTc 1 1 AclI AAcgtt 1 1 Aset ATtaat 1 1 BsmI GAATGCN 1 1 BspEI Tccgga 1 1 HC FR1 BstXI CCANNNNNntgg 1 1 HC FR2 DrdI GACNNNNnngtc 1 1 HindIII Aagctt 1 1 PciI Acatgt 1 1 SapI gaagagc 1 1 ScaI AGTact 1 1 SexAI Accwggt 1 1 SpeI Actagt 1 1 TliI Ctcgag 1 1 XhoI Ctcgag 1 1 BcgI cgannnnnntgc 2 2 BlpI GCtnagc 2 2 BssSI Ctcgtg 2 2 BstAPI GCANNNNntgc 2 2 EspI GCtnagc 2 2 KasI Ggcgcc 2 2 PflMI CCANNNNntgg 2 2 XmnI GAANNnnttc 2 2 ApaLI Gtgcac 3 3 LC signal seq NaeI GCCggc 3 3 NgoMI Gccggc 3 3 PvuII CAGctg 3 3 RsrII CGgwccg 3 3 BsrBI GAGcgg 4 4 BsrDI GCAATGNNn 4 4 BstZl7I GTAtac 4 4 EcoRI Gaattc 4 4 SphI GCATGc 4 4 SspI AATatt 4 4 AccI GTmkac 5 5 BclI Tgatca 5 5 BsmBI Nnnnnngagacg 5 5 BsrGI Tgtaca 5 5 DraI TTTaaa 6 6 NdeI CAtatg 6 6 HC FR4 SwaI ATTTaaat 6 6 BamHI Ggatcc 7 7 SacI GAGCTc 7 7 BciVI GTATCCNNNNNN 8 8 BsaBI GATNNnnatc 8 8 NsiI ATGCAt 8 8 Bsp120I Gggccc 9 9 CH1 ApaI GGGCCc 9 9 CH1 PsPOOMI Gggccc 9 9 BspHI Tcatga 9 11 ECoRV GATatC 9 9 AhdI GACNNNnngtc 11 11 BbsI GAAGAC 11 14 PsiI TTAtaa 12 12 BsaI GGTCTCNnnnn 13 15 XmaI Cccggg 13 14 AvaI Cycgrg 14 16 BglI GCCNNNNnggc 14 17 AlwNI CAGNNNctg 16 16 BspMI ACCTGC 17 19 XcmI CCANNNNNnnnntgg 17 26 BstEII Ggtnacc 19 22 HC FR4 Sse8387I CCTGCAgg 20 20 AvrII Cctagg 22 22 HincII GTYrac 22 22 BsgI GTGCAG 27 29 MscI TGGcca 30 34 BseRI NNnnnnnnnnctcctc 32 35 Bsu36I CCtnagg 35 37 PstI CTGCAg 35 40 EciI nnnnnnnnntccgcc 38 40 PpuMI RGgwccy 41 50 StyI Ccwwgg 44 73 Eco0109I RGgnccy 46 70 Acc65I Ggtacc 50 51 KpnI GGTACc 50 51 BpmI ctccag 53 82 AvaII Ggwcc 71 124

[0142] TABLE 2 Cleavage of 79 human heavy chains Planned location Enzyme Recognition Nch Ns of site AfeI AGCgct 0 0 AflII Cttaag 0 0 HC FR3 AscI GGcgcgcc 0 0 After LC BsiWI Cgtacg 0 0 BspDI ATcgat 0 0 BssHII Gcgcgc 0 0 FseI GGCCGGcc 0 0 HpaI GTTaac 0 0 NheI Gctagc 0 0 HC Linker NotI GCggccgc 0 0 In linker, HC/ anchor NruI TCCcga 0 0 NsiI ATGCAt 0 0 PacI TTAATtaa 0 0 PciI Acatgt 0 0 PmeI GTTTaaac 0 0 PvuI CGATcg 0 0 RsrII CGgwccg 0 0 SapI gaagagc 0 0 SfiI GGCCNNNNnggcc 0 0 HC signal seq SgfI GCGATcgc 0 0 SwaI ATTTaaat 0 0 AclI AAcgtt 1 1 AgeI Accggt 1 1 AseI ATtaat 1 1 AvrII Cctagg 1 1 BsmI GAATGCN 1 1 BsrBI GAGcgg 1 1 BsrDI GCAATGNNn 1 1 DraI TTTaaa 1 1 FspI TGCgca 1 1 HindIII Aagctt 1 1 MfeI Caattg 1 1 HC FR1 NaeI GCCggc 1 1 NgoMI Gccggc 1 1 SpeI Actagt 1 1 Acc65I Ggtacc 2 2 BstBI TTcgaa 2 2 KpnI GGTACc 2 2 MluI Acgcgt 2 2 NcoI Ccatgg 2 2 In HC signal seq NdeI CAtatg 2 2 HC FR4 PmlI CACgtg 2 2 XcmI CCANNNNNnnnntgg 2 2 BcgI cgannnnnntgc 3 3 BclI Tgatca 3 3 BglI GCCNNNNnggc 3 3 BsaBI GATNNnnatc 3 3 BsrGI Tgtaca 3 3 SnaBI TACgta 3 3 Sse8387I CCTGCAgg 3 3 ApaLI Gtgcac 4 4 LC Signal/FR1 BspHI Tcatga 4 4 BssSI Ctcgtg 4 4 PsiI TTAtaa 4 5 SphI GCATGc 4 4 AhdI GACNNNnngtc 5 5 BspEI Tccgga 5 5 HC FR1 MscI TGGcca 5 5 SacI GAGCTc 5 5 ScaI AGTact 5 5 SexAI Accwggt 5 6 SspI AATatt 5 5 TliI Ctcgag 5 5 XhoI Ctcgag 5 5 BbsI GAAGAC 7 8 BstAPI GCANNNNntgc 7 8 BstZl7I GTAtac 7 7 EcoRV GATatc 7 7 EcoRI Gaattc 8 8 BlpI GCtnagc 9 9 Bsu36I CCtnagg 9 9 DraIII CACNNNgtg 9 9 EspI Gctriagc 9 9 StuI AGGcct 9 13 XbaI Tctaga 9 9 HC FR3 Bsp120I Gggccc 10 11 CH1 ApaI GGGCCC 10 11 CH1 PspOOMI Gggccc 10 11 BciVI GTATCCNNNNNN 11 11 SalI Gtcgac 11 12 DrdI GACNNNNnngtc 12 12 KasI Ggcgcc 12 12 XmaI Cccggg 12 14 BglII Agatct 14 14 HincII GTYrac 16 18 BamHI Ggatcc 17 17 PflMI CCANNNNntgg 17 18 BsmBI Nnnnnngagacg 18 21 BstXI CCANNNNNntgg 18 19 HC FR2 XmnI GAANNnnttc 18 18 SacII CCGCgg 19 19 PstI CTGCAg 20 24 PvuII CAGctg 20 22 AvaI Cycgrg 21 24 EagI Cggccg 21 22 AatII GACGTc 22 22 BspMI ACCTGC 27 33 AccI GTmkac 30 43 StyI Ccwwgg 36 49 AlwNI CAGNNNctg 38 44 BsaI GGTCTCNnnnn 38 44 PpuMI RGgwccy 43 46 BsgI GTGCAG 44 54 BseRI NNnnnnnnnnctcctc 48 60 EciI nnnnnnnnntccgcc 52 57 BstEII Ggtnacc 54 61 HC Fr4, 47/79 have one EcoOl09I RGgnccy 54 86 BpmI ctccag 60 121 AvaII Ggwcc 71 140

[0143] TABLE 5 Use of FokI as “Universal Restriction Enzyme”

[0144] TABLE 8 Matches to URE FR3 adapters in 79 human HC. A. List of Heavy-chains genes sampled AF008566 AF035043 AF103026 af103033 AF103061 AF103072 af103078 AF103099 AF103102 AF103103 AF103174 AF103186 af103187 AF103195 af103277 af103286 AF103309 af103343 AF103367 AF103368 AF103369 AF103370 af103371 AF103372 AF158381 E05213 E05886 E05887 HSA235661 HSA235664 HSA235660 HSA235659 HSA235678 HSA235677 HSA235676 HSA235675 HSA235674 HSA235673 HSA240559 HSCB201 HSIGGVHC HSU44791 HSU44793 HSU82771 HSU82949 HSU82950 HSU82952 HSU82961 HSU86522 HSU86523 HSU92452 HSU94412 HSU94415 HSU94416 HSU94417 HSU94418 HSU96389 HSU96391 HSU96392 HSU96395 HSZ93849 HSZ93850 HSZ93851 HSZ93853 HSZ93855 HSZ93857 HSZ93860 HSZ93863 MCOMFRAA MCOMFRVA S82745 S32764 S83240 SABVH369 SADEIGVH SAH2IGVH SDA3IGVH SIGVHTTD SUK4IGVH

[0145] TABLE 8 B Testing all distinct GLGs from bases 89.1 to 93.2 of the heavy variable domain Id Nb 0 1 2 3 4 SEQ ID NO: 1 38 15 11 10 0 2 Seq1 gtgtattactgtqc 25 2 19 7 6 4 2 0 Seq2 gtAtattactgtgc 26 3 1 0 0 1 0 0 Seq3 gtgtattactgtAA 27 4 7 1 5 1 0 0 Seq4 gtgtattactgtAc 28 5 0 0 0 0 0 0 Seq5 Ttgtattactgtgc 29 6 0 0 0 0 0 0 Seq6 TtgtatCactgtgc 30 7 3 1 0 1 1 0 Seq7 ACAtattactgtgc 31 8 2 0 2 0 0 0 Seq8 ACgtattactgtgc 32 9 9 2 2 4 1 0 Seq9 ATgtattactcTtQc 33 Group 26 26 21 4 2 Cumulative 26 52 73 77 79

[0146] TABLE 8C Most important URE recognition seqs in FR3 Heavy 1 VHSzy1 GTGtattactgtgc (ON_SHC103) (SEQ ID NO:25) 2 VHSzy2 GTAtattactgtgc (ON_SHC323) (SEQ ID NO:26) 3 VHSzy4 GTGtattactgtac (ON_SHC349) (SEQ ID NO:28) 4 VHSzy9 ATctattactgtgc (ON_SHC5a) (SEQ ID NO:33)

[0147] TABLE 8D testing 79 human HC V genes with four probes Number of sequences . . .    79 Number of bases . . . 29143 Number of mismatches Id Best 0 1 2 3 4 5 1 39 15 11 10 1 2 0 Seq1 gtgtattactgtgc (SEQ ID NO:25) 2 22 7 6 5 3 0 1 Seq2 gtAtattactgtgc (SEQ ID NO:26) 3 7 1 5 1 0 0 0 Seq4 gtgtattactgtAc (SEQ ID NO:28) 4 11 2 4 4 1 0 0 Seq9 ATgtattactgtgc (SEQ ID NO:33) Group 25 26 20 5 2 Cumulative 25 51 71 76 78

[0148] One sequence has five mismatches with sequences 2, 4, and 9; it is scored as best for 2.

[0149] Id is the number of the adapter.

[0150] Best is the number of sequence for which the identified adapter was the best available.

[0151] The rest of the table shows how well the sequences match the adapters. For example, there are 11 sequences that match VHSzy1(Id=1) with 2 mismatches and are worse for all other adapters. In this sample, ⁹⁰% come within 2 bases of one of the four adapters. TABLE 130 PCR primers for amplification of human Ab genes (HuIgMFOR)      5′-tgg aag agg cac gtt ctt ttc ttt-3′ !(HuIgMFOREtop)5′-aaa gaa aag aac gtg cct ctt cca-3′=reverse complement (HuCkFOR)       5′-aca ctc tcc cct gtt gaa gct ctt-3′ (HuCL2FOR)      5′-tga aca ttc tgt agg ggc cac tg-3′ (HuCL7FOR)      5′-aga gca ttc tgc agg ggc cac tg-3′ ! Kappa (CKForeAsc)  5′-acc gcc tcc acc ggg cgc gcc tta tta aca ctc tcc cct gtt-               gaa gct ctt-3′ (CL2ForeAsc)    5′-acc gcc tcc acc ggg cgc gcc tta tta tga aca ttc tgt-               agg ggc cac (CL7ForeAsc)    5′-acc gcc tcc acc ggg cgc gcc tta tta aga gca ttc tgc-                 agg ggc cac tg-3′

[0152] TABLE 195 Human GLG FR3 sequences ! VH1 ! 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 agg gtc acc atg acc agg gac acg tcc atc agc aca gcc tac atg 81  82  82a 82b 82c 83  84  85  86  87  88  89  90  91  92 gag ctg agc agg ctg aga tct gac gac acg gcc gtg tat tac tgt 93  94  95 gcg aga ga ! 1-02# 1 aga gtc acc att acc agg gac aca tcc gcg agc aca gcc tac atg gag ctg agc agc ctg aga tct gaa gac acg gct gtg tat tac tgt gcg aga ga ! 1-03# 2 aga gtc acc atg acc agg aac acc tcc ata agc aca gcc tac atg gag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgt gcg aga gg ! 1-08# 3 aga gtc acc atg acc aca gac aca tcc acg agc aca gcc tac atg gag ctg agg agc ctg aga tct gac gac acg gcc gtg tat tac tgt gcg aga ga ! 1-18# 4 aga gtc acc atg acc gag gac aca tct aca gac aca gcc tac atg gag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgt gca aca ga ! 1-24# 5 aga gtc acc att acc agg gac agg tct atg agc aca gcc tac atg gag ctg agc agc ctg aga tct gag gac aca gcc atg tat tac tgt gca aga ta ! 1-45# 6 aga gtc acc atg acc agg gac acg tcc acg agc aca gtc tac atg gag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgt gcg aga ga ! 1-46# 7 aga gtc acc att acc agg gac atg tcc aca agc aca gcc tac atg gag ctg agc agc ctg aga tcc gag gac acg gcc gtg tat tac tgt gcg gca ga ! 1-58# 8 aga gtc acg att acc gcg gac gaa tcc acg agc aca gcc tac atg gag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgt gcg aga ga ! 1-69#9 aga gtc acg att acc gcg gac aaa tcc acg agc aca gcc tac atg gag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgt gcg aga ga ! 1-3# 10 aga gtc acc ata acc gcg gac acg tct aca gac aca gcc tac atg gag ctg agc agc ctg aga tct gag gac acg gcc gtg tat tac tgt gca aca ga ! 1-f# 11 VH2 agg ctc acc atc acc aag gac acc tcc aaa aac cag gtg gtc ctt aca atg acc aac atg gac cct gtg gac aca gcc aca tat tac tgt gca cac aga c! 2-05# 12 agg ctc acc atc tcc aag gac acc tcc aaa agc cag gtg gtc ctt acc atg acc aac atg gac cct gtg gac aca gcc aca tat tac tgt gca cgg ata c! 2-05# 12 agg ctc acc atc tcc aag gac acc tcc aaa agc cag gtg gtc ctt acc atg acc aac atg gac cct gtg gac aca gcc aca tat tac tgt gca cgg ata c! 2-26# 13 agg ctc acc atc tcc aag gac acc tcc aaa aac cag gtg gtc ctt aca atg acc aac atg gac cct gtg gac aca gcc acg tat tac tgt gca cgg ata c! 2-70# 14 VH3 cga ttc aac atc tcc aga gac aac gcc aag aac tca ctg tat ctg caa atg aac agc ctg aga gcc gag gac acg gct gtg tat tac tgt gcg aga ga ! 3-07# 15 cga ttc acc atc tcc aga gac aac gcc aag aac tcc ctg tat ctg caa atg aac agt ctg aga gct gag gac acg gcc ttg tat tac tgt gca aaa gat 1! 3-09#16 cga ttc acc atc tcc agg gac aac gcc aag aac tca ctg tat ctg caa atg aac agc ctg aga gcc gag gac acg gcc gtg tat tac tgt gcg aga ga ! 3-11# 17 cga ttc acc atc tcc aga gaa aat gcc aag aac tcc ttg tat ctt caa atg aac agc ctg aga gcc ggg gac acg gct gtg tat tac tgt gca aga ga ! 3-13# 18 aga ttc acc atc tca aga gat gat tca aaa aac acg ctg tat ctg caa atg aac agc ctg aaa acc gag gac aca ggg gtg tat tac tgt acc aca ga ! 3-15# 19 cga ttc acc atc tcc aga gac aac gcc aag aac tcc ctg tat ctg caa atg aac agt ctg aga gcc gag gac acg gcc ttg tat cac tgt gcg aga ga ! 3-20# 20 cga ttc acc atc tcc aga gac aac gcc aag aac tca ctg tat ctg caa atg aac agc ctg aga gcc gag gac acg gct gtg tat tac tgt gcg aga ga ! 3-21# 21 cgg ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctg caa atg aac agc ctg aga gcc gag gac acg gcc gta tat tac tgt gcg aaa ga ! 3-23# 22 cga ttc aac atc tcc aga gac aat tcc aag aac acg ctg tat ctg caa atg aac agc ctg aga gct gag gac acg gct gtg tat tac tgt gcg aaa ga ! 3-30# 23 cga ttc aac atc tcc aga gac aat tcc aag aac acg ctg tat ctg caa atg aac agc ctg aga gct gag gac acg gct gtg tat tac tgt gcg aga ga ! 3303# 24 cga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctg caa atg aac agc ctg aga gcc gag gac acg gct gtg tat tac tgt gcg aga ga ! 3305# 25 cga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctg caa atg aac agc ctg aga gcc gag gac acg gct gtg tat tac tgt gcg aga ga ! 3-33# 26 cga ttc acc atc tcc aga gac aac agc aaa aac tcc ctg tat ctg caa atg aac agt ctg aga act gag gac acc gcc ttg tat tac tgt gca aaa gat a! 3-43#27 cga ttc acc atc tcc aga gac aat gcc aag aac tca ctg tat ctg caa atg aac agc ctg aga gac gag gac acg gct gtg tat tac tgt gcg aga ga ! 3-48# 28 aga ttc acc atc tca aga gat ggt tcc aaa agc atc gcc tat ctg caa atg aac agc ctg aaa acc gag gac aca gcc gtg tat tac tgt act aga ga ! 3-49# 29 cga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctt caa atg aac agc ctg aga gcc gag gac acg gcc gtg tat tac tgt gcg aga ga ! 3-53# 30 aga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctt caa atg ggc agc ctg aga gct gag gac atg gct gtg tat tac tgt gcg aga ga ! 3-64# 31 aga ttc acc atc tcc aga gac aat tcc aag aac acg ctg tat ctt caa atg aac agc ctg aga gct gag gac acg gct gtg tat tac tgt gcg aga ga ! 3-66# 32 aga ttc acc atc tca aga gat gat tca aag aac tca ctg tat ctg caa atg aac agc ctg aaa acc gag gac acg gcc gtg tat tac tgt gct aga ga ! 3-72# 33 agg ttc acc atc tcc aga gat gat tca aag aac acg gcg tat ctg caa atg aac agc ctg aaa acc gag gac acg gcc ctg tat tac tgt act aga ca · 3-73# 34 cga ttc acc atc tcc aga gac aac gcc aag aac acg ctg tat ctg caa atg aac agt ctg aga gcc gag gac acg gct gtg tat tac tgt gca aga ga ! 3-74# 35 aga ttc acc atc tcc aga gac aat tcc aag aac acg ctg cat ctt caa atg aac agc ctg aga gct gag gac acg gct gtg tat tac tgt aag aaa ga ! 3-d#36 VH4 cga gtc acc ata tca gta gac aag tcc aag aac cag ttc tcc ctg aag ctg agc tct gtg acc gcc gcg gac acg gcc gtg tac tac tgt gcg aga ga ! 4-04# 37 cga gtc acc atg tca gta gac acg tcc aag aac cag ttc tcc ctg aag ctg agc tct gtg acc gcc gtg gac acg gcc gtg tat tac tgt gcg aga aa ! 4-28 # 38 cga gtt acc ata tca gta gac acg tct aag aac cag ttc tcc ctg aag ctg agc tct gtg act gcc gcg gac acg gcc gtg tat tac tgt gcg aga ga ! 4301# 39 cga gtc acc ata tca gta gac agg tcc aag aac cag ttc tcc ctg aag ctg agc tct gtg acc gcc gcg gac acg gcc gtg tat tac tgt gcc aga ga ! 4302# 40 cga gtt acc ata tca gta gac acg tcc aag aac cag ttc tcc ctg aag ctg agc tct gtg act gcc gca gac acg gcc gtg tat tac tgt gcc aga ga ! 4304# 41 cga gtt acc ata tca gta gac acg tct aag aac cag ttc tcc ctg aag ctg agc tct gtg act gcc gcg gac acg gcc gtg tat tac tgt gcg aga ga ! 4-31# 42 cga gtc acc ata tca gta gac acg tcc aag aac cag ttc tcc ctg aag ctg agc tct gtg acc gcc gcg gac acg gct gtg tat tac tgt gcg aga ga !4-34# 43 cga gtc acc ata tcc gta gac acg tcc aag aac cag ttc tcc ctg aag ctg agc tct gtg acc gcc gca gac acg gt gtg tat tac tgt gcg aga ca ! 4-39#10 44 cga gtc acc ata tca gta gac acg tcc aag aac cag ttc tcc ctg aag ctg agc tct gtg acc gct gcg gac acg gcc gtg tat tac tgt gcg aga ga ! 4-59# 45 cga gtc acc ata tca gta gac acg tcc aag aac cag ttc tcc ctg aag ctg agc tct gtg acc gct gcg gac acg gcc gtg tat tac tgt gcg aga ga ! 4-61# 46 cga gtc acc ata tca gta gac acg tcc aag aac cag ttc tcc ctg aag ctg agc tct gtg acc gcc gca gac acg gcc gtg tat tac tgt gcg aga ga ! 4-b# 47 ! VH5 cag gtc acc atc tca gcc gac aag tcc atc agc acc gcc tac ctg cag tgg agc agc ctg aag gcc tcg gac acc gcc atg tat tac tgt gcg aga ca ! 5-51# 48 cac gtc acc atc tca gct gac aag tcc atc agc act gcc tac ctg cag tgg agc agc ctg aag gcc tcg gac acc gcc atg tat tac tgt gcg aga  ! 5-a# 49 ! VH6 cga ata acc atc aac cca gac aca tcc aag aac cag ttc tcc ctg cag ctg aac tct gtg act ccc gag gac acg gct gtg tat tac tgt gca aga ga ! 6-1# 50 ! VH7 cgg ttt gtc ttc tcc ttg gac acc tct gtc agc acg gca tat ctg cag atc tgc agc cta aag gct gag gac act gcc gtg tat tac tgt gcg aga ga ! 71.1# 51

[0153] TABLE 250 REdaptors, Extenders, and Bridges used for Cleavage and Capture of Human Heavy Chains in FR3. A: BpYCH4V Probes of actual human BC genes  !HpyCH4V in FR3 of human HC, bases35-56; only those with TGca site TGca; 10, RE recognition:tgca of length 4 is expected at 10   1 6-1 agttctccctgcagctgaactc   2 3-11, 3-07, 3-21, 3-72, 3-48 cactgtatctgcaaatgaacag   3 3-09, 3-43, 3-20 ccctgtatctgcaaatgaacag   4 5-51 ccgcctacctgcagtggagcag   5 3-15, 3-30, 3-30.5, 2-30.3, 3-74, 3-23, 3-33 cgctgtatctgcaaatgaacag   6 7-4.1 cggcatatctgcagatctgcag   7 3-73 cggcgtatctgcaaatgaacag   8 5-a ctgcctacctgcagtggagcag   9 3-49 tcgcctatctgcaaatgaacag B: HpyCH4V REdaptors, Extenders, and Bridges  B.1 REdaptors  ! Cutting HC lower strand:  ! TmKeller for 100 mM NaCl, zero formamide  ! Edapters for cleavage T_(m) ^(W) T_(m) ^(K) (ON_HCFR36-1) 5′-agttctcccTGCAgctgaactc-3′ 68.0 64.5 (ON_HCFR36-1A) 5′-ttctcccTGCAgctgaactc-3′ 62.0 62.5 (ON_HCFR36-1B) 5′-ttctcccTGCAgctgaac-3′ 56.0 59.9 (ON_HCFR33-15) 5′-cgctgtatcTGCAaatgaacag-3′ 64.0 60.8 (ON_HCFR33-15A) 5′-ctgtatcTGCAaatgaacag-3′ 56.0 56.3 (ON_HCFR33-15B) 5′-ctgtatcTGCAaatgaac-3′ 50.0 53.1 (ON_HCER33-11) 5′-cactgtatcTcCAaatgaacag-3′ 62.0 58.9 (ON_HCFR35-51) 5′-ccgcctaccTGCAgtggagcag-3′ 74.0 70.1 !  B.2 Segment of synthetic 3-23 gene into which captured CDR3 is to be cloned !                    XbaI... !D323*  cgCttcacTaag tcT aga gac aaC tcT aag aaT acT ctC taC !       scab........ designed gene 3-23 gene................. ! !    HpyCH4V !     .. ..           AflII... !    Ttg caG atg aac agc TtA agG . . . !    ............................ . . . !  B.3 Extender and Bridges !Extender (bottom strand): ! (ON_HCHpyEx01)  5′-cAAgTAgAgAgTATTcTTAgAgTTgTcTcTAgAcTTAgTgAAgcg-3′ ! ON _(—) HCHpyEx01 is the reverse complement of ! 5′-cgCttcacTaag tcT aga gac aaC tcT aag aaT acT ctC taC Ttg-3′ ! ! Bridges (top strand, 9-base overlap): ! (ON_HCHpyBr016-1)   5′-cgCttcacTaag tCT aga gac aaC tcT aag-                   aaT acT ctC taC Ttg CAgctgaac-3′ {3′-term C is blocked} ! ! 3-15 et al. + 3-11 (ON_HCHpyBr023-15) 5′-cgCttcacTaag tcT aga gac aaC tcT aag-                   aaT acT ctC taC Ttg CAaatgaac-3′ {3′-term C is blocked} ! ! 5-51 (ON_HCHpyBr045-51)  5′-cgCttcacTaag tcT aga gac aaC tcT aag-                    aaT acT ctC taC Ttg CAgtggagc-3′ {3′-term C is blocked} ! ! PCR primer (top strand) ! (ON_HCHpyPCR)        5′-cgCttcacTaag tcT aga gac-3′ ! C: BlpI Probes from human HC GLGs    1 1-58,1-03,1-08,1-69,1-24,1-45,1-46,1-f, 1−e acatggaGCTGAGCagcctgag    2 1-02 acatggaGCTGAGCaagctgag    3 1-18 acatggagctgaggagcctgag    4 5-51,5-a acctgcagtggagcagcctgaa    5 3-15,3-73,3-49,3-72 atctgcaaatgaacagcctgaa    6 3303,3-33,3-07,3-11,3-30,3-21,3-23,3305,3-48 atctgcaaatgaacagcctgag    7 3-20,3-74,3-09, 3-43 atctgcaaatgaacagtctgag    8 74.1 atctgcagatctgcagcctaaa    9 3-66, 3-13, 3-53, 3-d atcttcaaatgaacagcctgag   10 3-64 atcttcaaatgggcagcctgag   11 4301,4-28,4302,4-04,4304,4-31,4-34,4-39,4-59,4-61,4-b ccctgaaGCTGAGCtctgtgac   12 6-1 ccctgcagctgaactctgtgac   13 2-70,2-05 tccttacaatgaccaacatgga   14 2-26 tccttaccatgaccaacatgga D: BlpI REdaptors, Extenders, and Bridges  D.1 REdaptors T_(m) ^(W) T_(m) ^(K) (BlpF3HC1-58) 5′-ac atg gaG CTG AGC agc ctg ag-3′ 70 66.4 (BlpF3HC6-1) 5′-cc ctg aag ctg agc tct gtg ac-3′ 70 66.4 ! BlpF3HC6-1 matches 4-30.1, not 6-1. D.2 Segment of synthetic 3-23 gene into which captured CDR3 is to be cloned !                                                                 BlpI !                    XbaI...                                       . ... ... !D323*  cgCttcacTaag TCT AGA gac aaC tcT aag aaT acT ctC taC Ttg caG atg aac ! !                    AflII... !                 agC TTA AGG D.3 Extender and Bridges ! Bridges (BlpF3Brl) 5′-cgCttcacTcag tcT aga gaT aaC AGT aaA aaT acT TtG-                  tac Ttg caG Ctg a|GC agc ctg-3′ (BlpF3Br2) 5′-cgCttcacTcag tcT aga gaT aaC AGT aaA aaT acT TtG-                 taC Ttg caG Ctg a|gc tct gtg-3′                                     | lower strand is cut here ! ! Extender (BlpF3Ext) 5′- TcAgcTgcAAgTAcAAAgTATTTTTAcTgTTATcTcTAgAcTgAgTgAAgcg-3′ ! BlpF3Ext is the reverse complement of: ! 5′-cgCttcacTcag tcT aga gaT aaC AGT aaA aaT acT TtG taC Ttg caG Ctg a-3′ ! (BlpF3PCR) 5′-cgCttcacTcag tcT aga gaT aaC-3′ E: HpyCH4III Distinct GLG sequences surrounding site, bases 77-98   1 102#1,118#4,146#7,169#9,1e#10,311#17,353#30,404#37,4301 ccgtgtattactgtgcgagaga   2 103#2, 307#15, 321#21, 3303#24,333#26,348#28, 364#31,366#32 ctgtgtattactgtgcgagaga   3 108#3 ccgtgtattactgtgcgagagg   4 124#5,1f#11 ccgtgtattactgtgcaacaga   5 145#6 ccatgtattactgtgcaagata   6 158#8 ccgtgtattactgtgcggcaga   7 205#12 ccacatattactgtgcacacag   8 226#13 ccacatattactgtgcacggat   9 270#14 ccacgtattactgtgcacggat  10 309#16,343#27 ccttgtattactgtgcaaaaga  11 313#18,374#35,61#50 ctgtgtattactgtgcaagaga  12 315#19 ccgtgtattactgtaccacaga  13 320#20 ccttgtatcactgtgcgagaga  14 323#22 ccgtatattactgtgcgaaaga  15 330#23,3305#25 ctgtgtattactgtgcgaaaga  16 349#29 ccgtgtattactgtactagaga  17 372#33 ccgtgtattactgtgctagaga  18 373#34 ccgtgtattactgtactagaca  19 3d#36 ctgtgtattactgtaagaaaga  20 428#38 ccgtgtattactgtgcgagaaa  21 4302#40,4304#41 ccgtgtattactgtgccagaga  22 439#44 ctgtgtattactgtgcgagaca  23 551#48 ccatgtattactgtgcgagaca  24 5a#49 ccatgtattactgtgcgaga F: HpyCH4III REdaptors, Extenders, and Bridges  F.1 REdaptors ! ONs for cleavage of HC(lower) in FR3(bases 77-97) ! For cleavage with HpyCH4III, Bst4CI, or TaaI ! cleavage is in lower chain before base 88. !    77 788 888 888 889 999 999 9 !    78 901 234 567 890 123 456 7 T_(m) ^(W) T_(m) ^(K) (H43.77.97.1-02#1) 5′-cc gtg tat tAC TGT gcg aga g-3′ 64 62.6 (H43.77.97.1-03#2) 5′-ct gtg tat tAC TGT gcg aga g-3′ 62 60.6 (H43.77.97.108#3) 5′-cc gtg tat tAC TGT gcg aga g-3′ 64 62.6 (H43.77.97.323#22) 5′-cc gta tat tac tgt gcg aaa g-3′ 60 58.7 (H43.77.97.330#23) 5′-ct gtg tat tac tgt gcg aaa g-3′ 60 58.7 (H43.77.97.439#44) 5′-ct gtg tat tac tgt gcg aga c-3′ 62 60.6 (H43.77.97.551#48) 5′-cc atg tat tac tgt gcg aga c-3′ 62 60.6 (H43.77.97.5a#49) 5′-cc atg tat tAC TGT gcg aga  3′ 58 58.3   F.2 Extender and Bridges ! XbaI and AflII Sites in bridges are bunged (H43.XABr1) 5′-ggtgtagtga-   |TCT|AGt|gac|aac|tct|aag|aat|act|ctc|tac|55g|cag|atg|-   |aac|agC|TTt|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat tgt gcg aga-3′ (H43.XABr2) 5′-ggtgtagtga-   |TCT|AGt|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|-   |aac|agC|TTt|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat tgt gcg aaa-3′ (H43.XAExt) 5′-ATAgTAgAcT gcAgTgTccT cAgcccTTAA gcTgTTcATc TgcAAgTAgA-                gAgTATTcTT AgAgTTgTcT cTAgATcAcT AcAcc-3′ !H43.XAExt is the reverse complement of !5′-ggtgtagtga- !  |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- !  |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat -3′ (H43.XAPcR) 5′-ggtgtagtga |TCT|AGA|gac|aac-3′ ! XbaI and AflII sites in bridges are bunged (H43.ABr1) 5′-ggtgtagtga-   |aac|agC|TTt|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat tgt gcg aga-3′ (H43.ABr2) 5′-ggtgtagtga-   |aac|aagC|TTt|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat tgt gcg aaa-3′ (H43.AExt)  5′- ATAgTAgAcTgcAgTgTccTcAgcccTTAAgcTgTTTcAcTAcAcc-3′ !(H43.AExt) is the reverse complement of 5′-ggtgtagtga- ′  |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat-3′ (H43.APCR)       5′-ggtgtagtga |aac|agC|TTA|AGg|gct|g-3′

[0154] (FOKIact) 5′-cAcATccgTg TTgTT cAcggATgTg-3′ (VHEx881) 5′-AATAgTAgAc TgcAgTgTcc TcAgcccTTA AgcTgTTcAT cTgcAAgTAg-             AgAgTATTcT TAgAgTTgTc TcTAgAcTTA gTgAAgcg-3′ ! note that VHEx881 is the reverse complement of the ON below !         [RC] 5′-cgCttcacTaag- !                 Scab........ !                 Synthetic 3-23 as in Table 206 !                 |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- !                  XbaI... !                 |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|t-3′ !                      AflII... (VHBA881)     5′-cgCttcacTaag-                  |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|-                  |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgt gcg ag-3′ (VHBB881)      5′-cgCttcacTaag-                |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|-              1  |aac|agC|TTA|AGg|gct|gag|gac|acT|GcA|Gtc|tac|tat|tgt Acg ag-3′ (VH881PCR) 5′-cgCttcacTaag|TCT|AGA|gac|aac-3′

[0155] TABLE 600 V3-23 VH framework with variegated codons shown ! ! /////////                   17  18  19  20  21  22 ! //////////                    A   Q   P   A   M   A ///////// 5′- ctg tct gaa cG GCC cag ccG GCC atg gcc 29 ///////// 3′-gac aga ctt gc cgg gtc ggc cgg tac cgg ! /////////    Scab.........SfiI............. ! ///////////////////////////////////////                         NgoMI... ! /////////////////////////////////////////                                NcoI.... ! ! //////////////////////////// FR1(DP47/V3-23)--------------- ! //////////////////////////// 23  24  25  26  27  28  29  30 ! /////////////////////////////  E   V   Q   L   L   E   S   G //////////////////////////// gaa|gtt|CAA|TTG|tta|gag|tct|ggt| 53 ! //////////////////////////// ctt|caa|gtt|aac|aat|ctc|aga|cca| ! ///////////////////////////////////        | MfeI  | ! ! --------------FR1 !  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !   G   G   L   V   Q   P   C   G   S   L   R   L   S   C   A |ggc|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta| cgt|ctt|tct|tgc|gct| 98 ! |ccg|cca|gaa|caa|gtc|gga|cca|cca|aga|aat|gca|gaa|aga|acg|cga| ! Sites to be varied--->       ***     ***     *** ! ----FR1---------------->|...CDR1................|---FR2------ !  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !   A   S   G   F   T   F   S   S   Y   A   M   S   W   V   R |gct|TCC|GGA|ttc|act|ttc|tct|tCG|TAC|Gct|atg|tct|tgg|gtt|cgC| 143 ! |cga|agg|cct|aag|tga|aag|aga|agc|atg|cga|tac|aga|acc|caa|gcg| !     | BspEI |                 | BsiWI|                     |BstXI. ! !                       Sites to be varies---> ***     *** *** ! -------FR2--------------------------------->|...CDR2........ ! 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !   Q   A   P   G   K   G   L   E   W   V   S   A   I   S   G |CAa|gct|ccT|GG t|aaa| ggt|ttg|gag|tgg|gtt|tct|gct|atc|tct|ggt| 188 ! |gtt|cga|gga|cca|ttt|cca|aac|ctc|acc|caa|aga|cga|tag|aga|cca| ! ...BstXI          | ! !              ***     *** ! .....CDR2............................................|---FR3--- !   76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !    S   G   G   S   T   Y   Y   A   D   S   V   K   G   R   F  |tct|ggt|ggc|agt|act|tac|tat|gct|gac|tcc|gtt|aaa|gg t|cgc|ttc| 233 !  |aga|cca|ccg|tca|tga|atg|ata|cga|ctg|agg|caa|ttt|cca|gcg|aag| ! ! --------FR3-------------------------------------------------- !   91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !   T   I   S   R   D   N   S   K   N   T   L   Y   L   Q   M |act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg| 278 ! |tga|tag|aga|tct|ctg|ttg|aga|ttc|tta|tga|gag|atg|aac|gtc|tac| !         | XbaI  | ! ! ---FR3----------------------------------------------------->| !  106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !   N   S   L   R   A   E   D   T   A   V   Y   Y   C   A   K |aac|a gC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgc|gct|aaa| 323 ! |ttg|tcg|aat|tcc|cga|ctc|ctg|tga|cgt|cag|atg|ata|acg|cga|ttt| !        |AflII |               | PstI | ! ! .......CDR3.................|----FR4------------------------- !  121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !   D   Y   E   G   T   G   Y   A   F   D   I   W   G   Q   G |gac|tat|gaa|ggt|act|ggt|tat|gct|ttc|gaC|ATA|TGg|ggt|c aa|ggt| 368 ! |ctg|ata|ctt|cca|tga|cca|ata|cga|aag|ctg|tat|acc|cca|gtt|cca| !                                        | NdeI | ! ! --------------FR4---------->| !  136 137 138 139 140 141 142 !   T   N   V   T   V   S   S |act|atG|GTC|ACC|gtc|tct|agt- 389 ! |tga|tac|cag|tgg|cag|aga|tca- !        | BstEII | ! ! /////////////// 143 144 145 146 147 148 149 150 151 152 ! ////////////////  A   S   T   K   G   P   S   V   F   P /////////////// gcc tcc acc aaG GGC CCa tcg GTC TTC ccc-3′ 419 ! /////////////// cgg agg tgg tta ccg ggt agc cag aag ggg -5′ ! ////////////// ///////////////               Bsp120I.      BbsI...(2/2) ! ////////////// ///////////////               ApaI.... ! (SFPRMET) 5′-ctg tct gaa cG GCC cag ccG-3′ (TOPFR1A) 5′-ctg tct gaa cG GCC cag ccG GCC atg gcc-    gaa|gtt|CAA|TTG|tta|gag|tct|ggt|-   |ggc|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta-3′ (BOTR1B)             3′-caa|gtc|gga|cca|cca|aga|aat|gca|gaa|aga|acg|cga|- |cga|agg|cct|aag|tga|aag-5′ ! bottom strand (BOTFR2) 3′-acc|caa|gcg|-   |gtt|cga|gga|cca|ttt|cca|aac|ctc|acc|caa|aga|-5′ ! bottom strand (BOTFR3) 3′-  a|cga|ctg|agg|caa|ttt|cca|gcg|aag|-   |tga|tag|aga|tct|ctg|ttg|aga|ttc|tta|tga|gag|atg|aac|gtc|tac|- |ttg|tcg|aat|tcc|cga|ctc|ctg|tga-5′ (F06)  5′-gC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgc|gct|aaa|- |gac|tat|gaa|ggt|act|ggt|tat|gct|ttc|gac|ATA|TGg|ggt|c-3′ (BOTFR4) 3′-cga|aag|ctg|tat|acc|cca|gtt|cca|-   |tga|tac|cag|tgg|cag|aga|tca-       cgg agg tgg ttc ccg ggt aga cag aag ggg-5′ ! bottom strand (BOTPRCPRIM)             3′-gg ttc ccg ggt agc cag aag ggg-5′ ! ! CDR1 diversity ! (ON-vgC1) 5′- |gct|TCC|GGA|tta|act|ttc|tct|<1>|TAC|<11>|atg|<1>|- !                             CDR1....................6859     |tgg|gtt|cgc|CAa|gct|ccT|GG -3′ ! !<1> stands for an equimolar mix of (ADEFGHIKLMNPQRSTVWY); no C !                              (this is not a sequence) ! CDR2 diversity ! (ON-vgC2) 5′-ggt|ttg|gag|tgg|gtt|tct|<2>|atc|<2>|<3>|- !                            CDR2............     |tct|ggt|ggc|<1>|act|<1>|tat|gct|gac|tcc|gtt|aaa|gg-3′ !     CDR2................................................ !<1> is an equimolar mixture of {ADEFGHIKLMNPQRSTVWT}; no C !<2> is an equimolar mixture of {YRWVGS}; no ACDEFHIKLMNPQT !<3> is an equimolar mixture of {PS}; no ACDEFGHIKLMNQRTVWY

[0156] TABLE 800 (new) The following list of enzymes was taken from http://rebase.neb.com/cgi-bin/asymmlist. I have removed the enzymes that a) cut within the recognition, b) cut on both sides of the recognition, or c) have fewer than 2 bases between recognition and closest cut site. REBASE Enzymes 04/13/2001 Type II Restriction Enzymes with Asymmetric Recognition Sequences: Enzymes Recognition Sequence Isoschizomers Suppliers AarI CACCTGCNNNN{circumflex over ( )}NNNN_ - y AceIII CAGCTCNNNNNNN{circumflex over ( )}NNNN_ - - Bbr7I GAAGACNNNNNNN{circumflex over ( )}NNNN_ - - BbvI GCAGCNNNNNNNN{circumflex over ( )}NNNN_ y BbvII GAAGACNN{circumflex over ( )}NNNN_ Bce83I CTTGAGNNNNNNNNNNNNNN_NN{circumflex over ( )} - - BceAI ACGGCNNNNNNNNNNNN{circumflex over ( )}NN_ - y BcefI ACGGCNNNNNNNNNNNN{circumflex over ( )}N_ - - BciVI GTATCCNNNNN_N{circumflex over ( )} BfuI y BfiI ACTGGGNNNN_N{circumflex over ( )} BmrI y BinI GGATCNNNN{circumflex over ( )}N_ BscAI GCATCNNNN{circumflex over ( )}NN_ - - BseRI GAGGAGNNNNNNNN_NN{circumflex over ( )} - y BsmFI GGGACNNNNNNNNNN{circumflex over ( )}NNNN_ BspLU11III y BspMI ACCTGCNNNN{circumflex over ( )}NNNN_ Acc36I y EciI GGCGGANNNNNNNNN_NN{circumflex over ( )} - y Eco57I CTGAAGNNNNNNNNNNNNNN_NN{circumflex over ( )} BspKT5I y FauI CCCGCNNNNNN_ BstFZ438I y FokI GGATGNNNNNNNNN{circumflex over ( )}NNNN_ BstPZ418I y GsuI CTGGAGNNNNNNNNNNNNNN_NN{circumflex over ( )} - y HgaI GACGCNNNNN{circumflex over ( )}NNNNN_ - y HphI GGTGANNNNNNN_N{circumflex over ( )} AsuHPI y MboII GAAGANNNNNNN_N{circumflex over ( )} - y MlyI GAGTCNNNNN{circumflex over ( )} SchI y MmeI TCCRACNNNNNNNNNNNNNNNNNN_NN{circumflex over ( )} - - MnlI CCTCNNNNNN_N{circumflex over ( )} - y PleI GAGTCNNNN{circumflex over ( )}N_ PpsI y RleAI CCCACANNNNNNNNN_NNN{circumflex over ( )} - - SfaNI GCATCNNNNN{circumflex over ( )}NNNN_ BspST5I y SspD5I GGTGANNNNNNNN{circumflex over ( )} - - Sth132I CCCGNNNN{circumflex over ( )}NNNN_ - - StsI GGATGNNNNNNNNNN{circumflex over ( )}NNNN - - TaqII GACCGANNNNNNNNN_NN{circumflex over ( )}, CACCCANNNNNNNNN_NN{circumflex over ( )} - - Tth111II CAARCANNNNNNNNN_NN{circumflex over ( )} - - UbaPI CGAACG - -

[0157] The notation is {circumflex over ( )} means cut the upper strand and _ means cut the lower strand. If the upper and lower strand are cut at the same place, then only {circumflex over ( )} appears. TABLE 120 MALIA3, annotated ! MALIA3 9532 bases !-------------------------------------------------------------------- 1 aat gct act act att agt aga att gat gcc acc ttt tca gct cgc gcc ! gene ii continued 49 cca aat gaa aat ata gct aaa cag gtt att gac cat ttg cga aat gta 97 tct aat ggt caa act aaa tct act cgt tcg cag aat tgg gaa tca act 145 gtt aca tgg aat gaa act tcc aga cac cgt act tta gtt gca tat tta 193 aaa cat gtt gag cta cag cac cag att cag caa tta agc tct aag cca 241 tcc gca aaa atg acc tct tat caa aag gag caa tta aag gta ctc tct 289 aat cct gac ctg ttg gag ttt gct tcc ggt ctg gtt cgc ttt gaa gct 337 cga att aaa acg cga tat ttg aag tct ttc ggg ctt cct ctt aat ctt 385 ttt gat gca atc cgc ttt gct tct gac tat aat agt cag ggt aaa gac 433 ctg att ttt gat tta tgg tca ttc tcg ttt tct gaa ctg ttt aaa gca 481 ttt gag ggg gat tca ATG aat att tat gac gat tcc gca gta ttg gac !     RBS?......      Start gene x, ii continues 529 gct atc cag tct aaa cat ttt act att acc ccc tct ggc aaa act tct 577 ttt gca aaa gcc tct cgc tat ttt ggt ttt tat cgt cgt ctg gta aac 625 gag ggt tat gat agt gtt gct ctt act atg cct cgt aat tcc ttt tgg 673 cgt tat gta tct gca tta gtt gaa tgt ggt att cct aaa tct caa ctg 721 atg aat ctt tct acc tgt aat aat gtt gtt ccg tta gtt cgt ttt att 769 aac gta gat ttt tct tcc caa cgt cct gac tgg tat aat gag cca gtt 817 ctt aaa atc gca TAA !                 End X & II 832 ggtaattca ca ! !  M1              E5                 Q10                 T15 843 ATG att aaa gtt gaa att aaa cca tct caa gcc caa ttt act act cgt ! Start gene V ! S17         S20                 P25                 E30 891 tct ggt gtt tct cgt cag ggc aag cct tat tca ctg aat gag cag ctt ! !         V35                 E40                 V45 939 tgt tac gtt gat ttg ggt aat gaa tat ccg gtt ctt gtc aag att act ! !     D50                 A55                 L60 987 ctt gat gaa ggt cag cca gcc tat gcg cct ggt cTG TAC Acc gtt cat !                                             BsrGI... ! L65                 V70                 S75                 R80 1035 ctg tcc tct ttc aaa gtt ggt cag ttc ggt tcc ctt atg att gac cgt ! !                 P85     K87 end of V 1083 ctg cgc ctc gtt ccg gct aag TAA C ! 1108 ATG gag cag gtc gcg gat ttc gac aca att tat cag gcg atg ! Start gene VII ! 1150 ata caa atc tcc gtt gta ctt tgt ttc gcg att ggt ata atc ! !                  VII and IX overlap. !                   ..... S2  V3  L4  V5                 S10 1192 gct ggg ggt caa agA TGA gt gtt tta gtg tat tct ttc gcc tct ttc gtt !                     End VII !                   |start IX ! L13     W15                 G20                 T25             E29 1242 tta ggt tgg tgc ctt cgt agt ggc att acg tat ttt acc cgt tta atg gaa ! 1293 act tcc tc ! !  .... stop of IX, IX and VIII overlap by four bases 1301 ATG aaa aag tct tta gtc ctc aaa gcc tct gta gcc gtt gct acc ctc ! Start signal sequence of viii. ! 1349 gtt ccg atg ctg tct ttc gct gct gag ggt gac gat ccc gca aaa gcg !                             mature VIII ---> 1397 gcc ttt aac tcc ctg caa gcc tca gcg acc gaa tat atc ggt tat gcg 1445 tgg gcg atg gtt gtt gtc att 1466 gtc ggc gca act atc ggt atc aag ctg ttt aag 1499 aaa ttc acc tcg aaa gca ! 1515 !  ...........  -35  .. ! 1517     agc tga taaaccgat acaattaaag gctccttttg !                ..... -10   ... 1552 gagccttttt ttttGGAGAt ttt ? S.D. underlined ! !      <------ III signal sequence --------------------------> !       M   K   K   L   L   F   A   I   P   L   V 1575 caac GTG aaa aaa tta tta ttc gca att cct tta gtt ! 1611 ! !  V   P   F   Y   S   H   S   A   Q 1612 gtt cct ttc tat tct cac aGT gcA Cag tCT !                          ApaLI... ! 1642 GTC GTG ACG CAG CCG CCC TCA GTG TCT GGG GCC CCA GGG GAG AGG GTC ACC ATC TCC TGC ACT GGG AGC AGC TCC AAC ATC GGG GCA !   BstEII... 1729 GGT TAT GAT GTA CAC TGG TAC CAG CAG CTT CCA GGA ACA GCC CCC AAA 1777 CTC CTC ATC TAT GGT AAC AGC AAT CGG CCC TCA GGG GTC CCT GAC CGA 1825 TTC TCT GGC TCC AAG TCT GGC ACC TCA GCC TCC CTG GCC ATC ACT 1870 GGG CTC CAG GCT GAG GAT GAG GCT GAT TAT 1900 TAG TGC CAG TCC TAT GAC AGC AGC CTG AGT 1930 GGC CTT TAT GTC TTC GGA ACT GGG ACC AAG GTC ACC GTC !                                       BstEII... 1969 CTA GGT CAG CCC AAG GCC AAC CCC ACT GTC ACT 2002 CTG TTC CCG CCC TCC TCT GAG GAG CTC CAA GCC AAC AAG GCC ACA CTA 2050 GTG TGT CTG ATC AGT GAC TTC TAC CCG GGA GCT GTG ACA GTG GCC TGG 2098 AAG GCA GAT AGC AGC CCC GTC AAG GCG GGA GTG GAG ACC ACC ACA CCC 2146 TCC AAA CAA AGC AAC AAC AAG TAC GCG GCC AGC AGC TAT CTG AGC CTG 2194 ACG CCT GAG CAG TGG AAG TCC CAC AGA AGC TAC AGC TGC CAG GTC ACG 2242 CAT GAA GGG AGC ACC GTG GAG AAG ACA GTG GCC CCT ACA GAA TGT TCA 2290 TAA TAA ACCG CCTCCACCGG GCGCGCCAAT TCTATTTCAA GGAGACAGTG ATA !                       AscI..... ! ! PelB signal----------------------------------------------> !  M   K   Y   L   L   P   T   A   A   A   C   L   L   L   L 2343 ATG AAA TAC CTA TTG CCT ACG GCA GCC GCT GGA TTG TTA TTA CTC ! !  16  17  18  19  20      21  22 !  A   A   Q   P   A       M   A 2388 gcG GCC cag ccG GCC     atg gcc !   SfiI............. !           NgoMI...(1/2) !                  NcoI......... ! !                             FR1 (DP47/V3-23)-------------- !                             23  24  25  26  27  28  29  30 !                              E   V   Q   L   L   E   S   G 2409                             gaa|gtt|CAA|TTG|tta|gag|tct|ggt| !                                    |MfeI  | ! ! --------------FR1-------------------------------------------- !  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !   G   G   L   V   Q   P   G   G   S   L   R   L   S   C   A 2433 |ggc|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta|cgt|ctt|tct|tgc|gct| ! ! ----FR1---------------->|...CDR1................|---FR2------ !  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60   A   S   G   F   T   F   S   S   Y   A   M   S   W   V   R 2478 |gct|TCC|GGA|ttc|act|ttc|tct|tCG|TAC|Gct|atg|tct|tgg|gtt|cgC| !     |BspEI |                 |BsiWI|                     |BstXI ! !      -------FR2-------------------------------->|...CDR2......... !      61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !       Q   A   P   G   K   G   L   E   W   V   S   A   I   S   G 2523     |CAa|gct|ccT|GGt|aaa|ggt|ttg|gag|tgg|gtt|tct|gct|atc|tct|ggt| ! ...BstXI          | ! ! .....CDR2............................................|---FR3--- !   76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !    S   C   C   S   T   Y   Y   A   D   S   V   K   G   R   F ! 2568  |tct|ggt|ggc|agt|act|tac|tat|gct|gac|tcc|gtt|aaa|ggt|cgc|ttc| ! ! ! --------FR3-------------------------------------------------- !   91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !   T   I   S   R   D   N   S   K   N   T   L   Y   L   Q   M 2613 |act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg| !         |XbaI  | ! ! ---FR3----------------------------------------------------->| !  106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !   N   S   L   R   A   E   D   T   A   V   Y   Y   C   A   K 2658 |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgc|gct|aaa| !        |AflII |               |PstI | ! ! .......CDR3.................|----FR4------------------------- !  121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !   D   Y   E   G   T   G   Y   A   F   D   I   W   G   Q   G 2703 |gac|tat|gaa|ggt|act|ggt|tat|gct|ttc|gaC|ATA|TGg|ggt|caa|ggt| !                                        |NdeI |(1/4) ! ! --------------FR4---------->| !  136 137 138 139 140 141 142 !   T   M   V   T   V   S   S 2748 |act|atG|GTC|ACC|gtc|tct|agt !        |BstEII | ! From BstEII onwards, pV323 is same as pCES1, except as noted. ! BstEII sites may occur in light chains; not likely to be unique in final ! vector. ! !                   143 144 145 146 147 148 149 150 151 152 !                    A   S   T   K   G   P   S   V   F   P 2769                   gcc tcc acc aaG GGC CCa tcg GTC TTC ccc !                                 Bsp120I.      BbsI...(2/2) !                                 ApaI.... ! ! 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 !  L   A   P   S   S   K   S   T   S   G   G   T   A   A   L 2799 ctg gca ccC TCC TCc aag agc acc tct ggg ggc aca gcg gcc ctg !           BseRI...(2/2) ! ! 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 !  G   C   L   V   K   D   Y   F   P   E   P   V   T   V   S 2844 ggc tgc ctg GTC AAG GAC TAC TTC CCc gaA CCG GTg acg gtg tcg !                                       AgeI.... ! ! 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 !  W   N   S   G   A   L   T   S   G   V   H   T   F   P   A 2889 tgg aac tca GGC GCC ctg acc agc ggc gtc cac acc ttc ccg gct !             KasI...(1/4) ! ! 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 !  V   L   Q   S   S   G   L   Y   S   I   S   S   V   V   T 2934 gtc cta cag tCt agc GGa ctc tac tcc ctc agc agc gta gtg acc !             (Bsu36I...)(knocked out) ! ! 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 !  V   P   S   S   S   L   G   T   Q   T   Y   I   C   N   V 2979 gtg ccC tCt tct agc tTG Ggc acc cag acc tac atc tgc aac gtg !         (BstXI...........)N.B. destruction of BstXI & BpmI sites. ! ! 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 !  N   H   K   P   S   N   T   K   V   D   K   K   V   E   P 3024 aat cac aag ccc agc aac acc aag gtg gac aag aaa gtt gag ccc ! ! 243 244 245 !  K   S   C   A   A   A   H   H   H   H   H   H   S   A 3069 aaa tct tgt GCG GCC GCt cat cac cac cat cat cac tct gct !             NotI...... ! !  E   Q   K   L   I   S   E   E   D   L   N   G   A   A 3111 gaa caa aaa ctc atc tca gaa gag gat ctg aat ggt gcc gca ! ! !  D   I   N   D   D   R   M     A   S    G   A 3153 GAT ATC aac gat gat cgt atg   gct AGC  ggc gcc ! rEK cleavage site..........   NheI...  KasI... ! EcoRV.. ! ! Domain 1 --------------------------------------------------------- !    A   E   T   V   E   S   C   L   A ! 3183   gct gaa act gtt gaa agt tgt tta gca ! ! !  K   P   H   T   E   I   S   F 3210 aaa ccc cat aca gaa aat tca ttt ! !  T   N   V   W   K   D   D   K   T 3234 aCT AAC GTC TGG AAA GAC GAC AAA ACt ! !  L   D   R   Y   A   N   Y   E   G   C   L   W   N   A   T   G   V 3261 tta gat cgt tac gct aac tat gag ggt tgt ctg tgG AAT GCt aca ggc gtt !                                               BsmI     ! !  V   V   C   T   G   D   E   T   Q   C   Y   G   T   W   V   P   I 3312 gta gtt tgt act ggt GAC GAA ACT GAG TGT TAC GGT ACA TGG GTT cct att ! !  G   L   A   I   P   E   N 3363 ggg ctt gct atc cct gaa aat ! ! L1 linker ------------------------------------- !  E   G   G   G   S   E   G   G   G   S 3384 gag ggt ggt ggc tct gag ggt ggc ggt tct ! !  E   G   G   G   S   E   G   G   G   T 3414 gag ggt ggc ggt tct gag ggt ggc ggt act ! ! Domain 2 --------------------------------------- 3444 aaa cct cct gag tac ggt gat aca cct att ccg ggc tat act tat atc aac 3495 cct ctc gac ggc act tat ccg cct ggt act gag caa aac ccc gct aat cct 3546 aat cct tct ctt GAG GAG tct cag cct ctt aat act ttc atg ttt cag aat !                 BseRI   3597 aat agg ttc cga aat agg cag ggg gca tta act gtt tat acg ggc act 3645 gtt act caa ggc act gac ccc gtt aaa act tat tac cag tac act cct 3693 gta tca tca aaa gcc atg tat gac gct tac tgg aac ggt aaa ttC AGA !                                                           AlwNI 3741 GAC TGc gct ttc cat tct ggc ttt aat gaa gat cca ttc gtt tgt gaa !  AlwNI 3789 tat caa ggc caa tcg tct gac ctg cct caa cct cct gtc aat gct ! 3834 ggc ggc ggc tct ! start L2 -------------------------------------------------------------- 3846 ggt ggt ggt tct 3858 ggt ggc ggc tct 3870 gag ggt ggt ggc tct gag ggt ggc ggt tct 3900 gag ggt ggc ggc tct gag gga ggc ggt tcc 3930 ggt ggt ggc tct ggt    ! end L2 ! ! Domain 3 --------------------------------------------------------------- !  S   G   D   F   D   Y   E   K   M   A   N   A   N   K   G   A 3945 tcc ggt gat ttt gat tat gaa aag atg gca aac gct aat aag ggg gct ! !  M   T   E   N   A   D   E   N   A   L   Q   S   D   A   K   G 3993 atg acc gaa aat gcc gat gaa aac gag cta cag tct gac gct aaa ggc ! !  K   L   D   S   V   A   T   D   Y   G   A   A   I   D   G   F 4041 aaa ctt gat tct gtc gct act gat tac ggt gat gct atc gat ggt ttc ! !  I   G   D   V   S   G   L   A   N   G   N   G   A   T   G   D 4089 att ggt gac gtt tcc ggc ctt gat aat ggt aat ggt gct act ggt gat ! !  F   A   G   S   N   S   Q   M   A   Q   V   G   D   G   D   N 4137 ttt gat ggc tat aat tcc caa atg gct caa gtc ggt gac ggt gat aat ! !  S   P   L   M   N   N   F   R   Q   Y   L   P   S   L   P   Q 4185 tca cat tta atg aat aat ttc cgt caa tat tta cct tcc atc cat caa ! !  S   V   E   C   R   P   F   V   F   S   A   G   K   P   Y   E 4233 tcg gtt gaa tgt cgc cct ttt gtc ttt aga gct ggt aaa cca tat gaa ! !  F   S   I   D   C   D   K   I   N   L   F   R 4281 ttt tct att gat tgt gac aaa ata aac tta tta cgt !                                             End Domain 3 ! !  G   V   F   A   F   L   L   Y   V   A   T   F   M   Y   V  F140 4317 ggt gtc ttt gcg ttt ctt tta tat gtt gcc aac ttt atg tat gta ttt ! start transmembrane segment ! !  S   T   F   A   N   I   L 4365 tat acg ttt gct aac ata ctg ! !  R   N   K   E   S 4386 cgt aat aag gag tct TAA ! stop of iii ! Intracellular anchor. ! !     M1  P2  V   L  L5   G   I   P   L  L10  L   R   F   L  G15 4404 tc ATG cca gtt ctt ttg ggt att ccg tta tta ttg cgt ttc ctc ggt !    Start VI ! 4451 ttc ctt ctg gta act ttg ttc ggc tat ctg ctt act ttt ctt aaa aag 4499 ggc ttc ggt aag ata gct att gct att tca ttg ttt ctt gct ctt att 4547 att ggg ctt aac tca att ctt gtg ggt tat ctc tct gat att agc gct 4595 caa tta ccc tct gac ttt gtt cag ggt gtt cag tta att ctc ccg tct 4643 aat gcg ctt ccc tgt ttt tat gtt att ctc tct gta aag gct gct att 4691 ttc att ttt gac gtt aaa caa aaa atc gtt tct tat ttg gat tgg gat ! !            M1  A2  V3      F5                 L10         G13 4739 aaa TAA t ATG gct gtt tat ttt gta act ggc aaa tta ggc tct gga !  end VI   Start gene I ! !  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28 !  K   T   L   V   S   V   G   K   I   Q   D   K   I   V   A 4785 aag acg ctc gtt agc gtt ggt aag att cag gat aaa att gta gct ! !  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43 !  G   C   K   I   A   T   N   L   D   L   R   L   Q   N   L 4830 ggg tgc aaa ata gca act aat ctt gat tta agg ctt caa aac ctc ! !  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58 !  P   Q   V   G   R   F   A   K   T   P   I   V   L   R   I 4875 ccg caa gtc ggg agg ttc gct aaa acg cct cgc gtt ctt aga ata ! !  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73 !  P   D   K   P   S   I   S   D   L   L   A   I   G   R   G 4920 ccg gat aag cct tct ata tct gat ttg ctt gct att ggg cgc ggt ! !  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88 !  N   D   S   Y   D   E   N   K   N   G   L   L   V   L   D 4965 aat gat tcc tac gat gaa aat aaa aac ggc ttg ctt gtt ctc gat ! !  89  90  91  92  93  94  95  96  97  98  99 100 101 102 103 !  E   C   G   T   W   F   N   T   R   S   W   N   D   K   E 5010 gag tgc ggt act tgg ttt aat acc cgt tct tgg aat gat aag gaa ! ! 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 !  R   Q   P   I   I   D   W   F   L   H   A   R   K   L   G 5055 aga cag ccg att att gat tgg ttt cta cat gct cgt aaa tta gga ! ! 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 !  W   D   I   I   F   L   V   Q   D   L   S   I   V   D   K 5100 tgg gat att att ttt ctt gtt cag gac tta tct att gtt gat aaa ! ! 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 !  Q   A   R   S   A   L   A   E   H   V   V   Y   C   R   R 5145 cag gcg cgt tct gca tta gct gaa cat gtt gtt tat tgt cgt cgt ! ! 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 !  L   D   R   I   T   L   P   F   V   G   T   L   Y   S   L 5190 ctg gac aga att act tta cct ttt gtc ggt act tta tat tct ctt ! ! 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 !  I   T   G   S   K   M   P   L   P   K   L   H   V   C   V 5235 att act ggc tcg aaa atg cct ctg cct aaa tta cat gtt ggc gtt ! ! 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 !  V   K   Y   G   D   S   Q   L   S   P   T   V   E   R   W 5280 gtt aaa tat ggc gat tct caa tta agc cct act gtt gag cgt tgg ! ! 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 !  L   Y   T   C   K   N   L   Y   N   A   Y   D   T   K   Q 5325 ctt tat act ggt aag aat ttg tat aac gca tat gat act aaa cag ! ! 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 !  A   F   S   S   N   Y   D   S   G   V   Y   S   Y   L   T 5370 gct ttt tct agt aat tat gat tcc ggt gtt tat tct tat tta acg ! ! 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 !  P   Y   L   S   H   G   R   Y   F   K   P   L   N   L   G 5415 cct tat tta tca cac ggt cgg tat ttc aaa cca tta aat tta ggt ! ! 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 !  Q   K   M   K   L   T   K   I   Y   L   K   K   F   S   R 5460 cag aag atg aaa tta act aaa ata tat ttg aaa aag ttt tct cgc ! ! 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 !  V   L   C   L   A   I   G   F   A   S   A   F   T   Y   S 5505 gtt ctt tgt ctt gcg att gga ttt gca tca gca ttt aca tat agt ! ! 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 !  Y   I   T   Q   P   K   P   E   V   K   K   V   V   S   Q 5550 tat ata acc caa cct aag ccg gag gtt aaa aag gta gtc tct cag ! ! 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 !  T   Y   D   F   D   K   F   T   I   D   S   S   Q   R   L 5595 acc tat gat ttt gat aaa ttc act att gac tct tct cag cgt ctt ! ! 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 !  N   L   S   Y   R   Y   V   F   K   D   S   K   G   K   L 5640 aat cta agc tat cgc tat gtt ttc aag gat tct aag gga aaa TTA !                                                         PacI ! !  314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 !   I   N   S   D   D   L   Q   K   Q   G   Y   S   L   T   Y 5685  ATT AAt agc gac gat tta cag aag caa ggt tat tca ctc aca tat ! PacI ! !  329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 !  i  I   D   L   C   T   V   S   I   K   K   G   N   S   N   E ! iv                                                       Ml  K 5730    att gat tta tgt act gtt tcc att aaa aaa ggt aat tca aAT Gaa !                                                         Start IV ! !     344 345 346 347 348 349 ! i    I   V   K   C   N   .End of I ! iv    L3  L   N5  V   I7  N    F  V10 5775     att gtt aaa tgt aat TAA T TTT GTT ! IV continued..... 5800 ttc ttg atg ttt gtt tca tca tct tct ttt gct cag gta att gaa atg 5848 aat aat tcg cct ctg cgc gat ttt gta act tgg tat tca aag caa tca 5896 ggc gaa tcc gtt att gtt tct ccc gat gta aaa ggt act gtt act gta 5944 tat tca tct gac gtt aaa cct gaa aat cta cgc aat ttc ttt att tct 5992 gtt tta cgt gct aat aat ttt gat atg gtt ggt tca att cct tcc ata 6040 att cag aag tat aat cca aac aat cag gat tat att gat gaa ttg cca 6088 tca tct gat aat cag gaa tat gat gat aat tcc gct cct tct ggt ggt 6136 ttc ttt gtt ccg caa aat gat aat gtt act caa act ttt aaa att aat 6184 aac gtt cgg gca aag gat tta ata cga gtt gtc gaa ttg ttt gta aag 6232 tct aat act tct aaa tcc tca aat gta tta tct att gac ggc tct aat 6280 cta tta gtt gtt TCT gca cct aaa gat att tta gat aac ctt cct caa !                  ApaLI removed 6328 ttc ctt tct act gtt gat ttg cca act gac cag ata ttg att gag ggt 6376 ttg ata ttt gag gtt cag caa ggt gat gct tta gat ttt tca ttt gct 6424 gct ggc tct cag cgt ggc act gtt gca ggc ggt gtt aat act gac cgc 6472 ctc acc tct gtt tta tct tct gct ggt ggt tcg ttc ggt att ttt aat 6520 ggc gat gtt tta ggg cta tca gtt cgc gca tta aag act aat agc cat 6568 tca aaa ata ttg tct gtg cca cgt att ctt acg ctt tca ggt cag aag 6616 ggt tct atc tct gtT GGC CAg aat gtc cct ttt att act ggt cgt gtg !                   MscI     6664 act ggt gaa tct gec aat gta aat aat cca ttt cag acg att gag cgt 6712 caa aat gta ggt att tcc atg agc gtt ttt cct gtt gca atg gct ggc 6760 ggt aat att gtt ctg gat att acc agc aag gcc gat agt ttg agt tct 6808 tct act cag gca agt gat gtt att act aat caa aga agt att gct aca 6856 acg gtt aat ttg cgt gat gga cag act ctt tta ctc ggt ggc ctc act 6904 gat tat aaa aac act tct caa gat tct ggc gta ccg ttc ctg tct aaa 6952 atc cct tta atc ggc ctc ctg ttt agc tcc cgc tct gat tcc aac gag 7000 gaa agc acg tta tac gtg ctc gtc aaa gca acc ata gta cgc gcc ctg 7048 TAG cggcgcatt ! End IV 7060 aagcgcggcg ggtgtggtgg ttacgcgcag cgtgaccgct acacttgcca gcgccctagc 7120 gcccgctcct ttcgctttct tccgttcctt tctcgccacg ttcGCCGGCt ttccccgtca !                                                NgoMI  7180 agctctaaat cgggggctcc ctttagggtt ccgatttagt gctttacggc acctcgaccc 7240 caaaaaactt gatttgggtg atggttCACG TAGTGggcca tcgccctgat agacggtttt !                             DraIII     7300 tcgccctttG ACGTTGGAGT Ccacgttctt taatagtgga ctcttgttcc aaactggaac !          DrdI           7360 aacactcaac cctatctcgg gctattcttt tgatttataa gggattttgc cgatttcgga 7420 accaccatca aacaggattt tcgcctgctg gggcaaacca gcgtggaccg cttgctgaaa 7480 ctctctcagg gccaggcggt gaagggcaat CAGCTGttgc cCGTCTCact ggtgaaaaga !                                  PvuII.      BsmBI. 7540 aaaaccaccc tGGATCC  AAGCTT !             BamHI   HindIII (1/2) !             Insert carrying bla gene 7563    gcaggtg gcacttttcg gggaaatgtg cgcggaaccc 7600 ctatttgttt atttttctaa atacattcaa atatGTATCC gctcatgaga caataaccct !                                      BciVI 7660 gataaatgct tcaataatat tgaaaaAGGA AGAgt !                             RBS.?... ! Start bla gene 7695 ATG agt att caa cat ttc cgt gtc gcc ctt att ccc ttt ttt gcg gca ttt 7746 tgc ctt cct gtt ttt gct cac cca gaa acg ctg gtg aaa gta aaa gat gct 7797 gaa gat cag ttg ggC gCA CGA Gtg ggt tac atc gaa ctg gat ctc aac agc !                      BssSI... !                  ApaLI removed 7848 ggt aag atc ctt gag agt ttt cgc ccc gaa gaa cgt ttt cca atg atg agc 7899 act ttt aaa gtt ctg cta tgt cat aca cta tta tcc cgt att gac gcc ggg 7950 caa gaG CAA CTC GGT CGc cgg gcg cgg tat tct cag aat gac ttg gtt gAG !       BcgI                                                       ScaI 8001 TAC Tca cca gtc aca gaa aag cat ctt acg gat ggc atg aca gta aga gaa ! ScaI  8052 tta tgc agt gct gcc ata aca atg agt gat aac act gcg gcc aac tta ctt 8103 ctg aca aCG ATC Gga gga ccg aag gag cta acc gct ttt ttg cac aac atg !          PvuI     8154 ggg gat cat gta act cgc ctt gat cgt tgg gaa ccg gag ctg aat gaa gcc 8205 ata cca aac gac gag cgt gac acc acg atg cct gta gca atg cca aca acg 8256 tTG CGC Aaa cta tta act ggc gaa cta ctt act cta gct tcc cgg caa caa !  FspI.... 8307 tta ata gac tgg atg gag gcg gat aaa gtt gca gga cca ctt ctg cgc tcg 8358 GCC ctt ccG GCt ggc tgg ttt att gct gat aaa tct gga gcc ggt gag cgt ! BglI           8409 gGG TCT Cgc ggt atc att gca gca ctg ggg cca gat ggt aag ccc tcc cgt !  BsaI     8460 atc gta gtt atc tac acG ACg ggg aGT Cag gca act atg gat gaa cga aat !                       AhdI            8511 aga cag atc gct gag ata ggt gcc tca ctg att aag cat tgg TAA ctgt !                                                         stop 8560 cagaccaagt ttactcatat atactttaga ttgatttaaa acttcatttt taatttaaaa 8620 ggatctaggt gaagatcctt tttgataatc tcatgaccaa aatcccttaa cgtgagtttt 8680 cgttccactg tacgtaagac cccc 8704 AAGCTT   GTCGAC tgaa tggcgaatgg cgctttgcct ! HindIII  SalI.. ! (2/2)    HincII 8740 ggtttccggc accagaagcg gtgccggaaa gctggctgga gtgcgatctt ! 8790 CCTGAGG ! Bsu36I  8797      ccgat actgtcgtcg tcccctcaaa ctggcagatg 8832 cacggttacg atgcgcccat ctacaccaac gtaacctatc ccattacggt caatccgccg 8892 tttgttccca cggagaatcc gacgggttgt tactcgctca catttaatgt tgatgaaagc 8952 tggctacagg aaggccagac gcgaattatt tttgatggcg ttcctattgg ttaaaaaatg 9012 agctgattta acaaaaattt aacgcgaatt ttaacaaaat attaacgttt acaATTTAAA !                                                           SwaI... 9072 Tatttgctta tacaatcttc ctgtttttgg ggcttttctg attatcaacc GGGGTAcat !                                                        RBS? 9131 ATG att gac atg cta gtt tta cga tta ccg ttc atc gat tct ctt gtt tgc ! Start gene II 9182 tcc aga ctc tca ggc aat gac ctg ata gcc ttt gtA GAT CTc tca aaa ata !                                               BglII... 9233 gct acc ctc tcc ggc atg aat tta tca gct aga acg gtt gaa tat cat att 9284 gat ggt gat ttg act gtc tcc ggc ctt tct cac cct ttt gaa tct tta cct 9335 aca cat tac tca ggc att gca ttt aaa ata tat gag ggt tct aaa aat ttt 9386 tat cct tgc gtt gaa ata aag gct tct ccc gca aaa gta tta cag ggt cat 9437 aat gtt ttt ggt aca acc gat tta gct tta tgc tct gag gct tta ttg ctt 9488 aat ttt gct aat tct ttg cct tgc ctg tat gat tta ttg gat gtt ! 9532 ! gene II continues

[0158] TABLE 120B Sequence of MALIA3, condensed LOCUS ORIGIN MALIA3 9532 CIRCULAR 1 AATGCTACTA CTATTAGTAG AATTGATGCC ACCTTTTCAG CTCGCGCCCC AAATGAAAAT 61 ATAGCTAAAC AGGTTATTGA CCATTTGCGA AATGTATCTA ATGCTCAAAC TAAATCTACT 121 CGTTCGCAGA ATTGGGAATC AACTGTTACA TGGAATCAAA CTTCCAGACA CCGTACTTTA 181 GTTGCATATT TAAAACATGT TGAGCTACAG CACCAGATTC AGCAATTAAG CTCTAAGCCA 241 TCCGCAAAAA TGACCTCTTA TCAAAAGGAG CAATTAAAGG TACTCTCTAA TCCTGACCTG 301 TTGGAGTTTG CTTCCGGTCT GGTTCGCTTT GAAGCTCGAA TTAAAACGCG ATATTTGAAG 361 TCTTTCGGGC TTCCTCTTAA TCTTTTTGAT GCAATCCGCT TTGCTTCTGA CTATAATAGT 421 CAGGGTAAAG ACCTGATTTT TGATTTATGG TCATTCTCGT TTTCTGAACT GTTTAAAGCA 481 TTTGAGGGGG ATTCAATGAA TATTTATGAC GATTCCGCAG TATTGGACGC TATCCAGTCT 541 AAACATTTTA CTATTACCCC CTCTGGCAAA ACTTCTTTTG CAAAAGCCTC TCGCTATTTT 601 GGTTTTTATC GTCGTCTGGT AAACGAGGGT TATGATAGTG TTGCTCTTAC TATGCCTCGT 661 AATTCCTTTT GGCGTTATGT ATCTGCATTA GTTGAATGTG GTATTCCTAA ATCTCAACTG 721 ATGAATCTTT CTACCTGTAA TAATGTTGTT CCGTTAGTTC GTTTTATTAA CGTAGATTTT 781 TCTTCCCAAC GTCCTGACTG GTATAATGAG CCAGTTCTTA AAATCGCATA AGGTAATTCA 841 CAATGATTAA AGTTGAAATT AAACCATCTC AAGCCCAATT TACTACTCGT TCTGGTGTTT 901 CTCGTCAGGG CAAGCCTTAT TCACTGAATG AGCAGCTTTG TTACGTTGAT TTGGGTAATG 961 AATATCCCGT TCTTGTCAAG ATTACTCTTG ATGAAGGTCA GCCAGCCTAT GCGCCTGGTC 1021 TGTACACCGT TCATCTGTCC TCTTTCAAAG TTGGTCAGTT CGGTTCCCTT ATGATTGACC 1081 GTCTGCGCCT CGTTCCGGCT AAGTAACATG GAGCAGGTCG CGGATTTCGA CACAATTTAT 1141 CAGGCGATGA TACAAATCTC CGTTGTACTT TGTTTCGCGC TTGGTATAAT CGCTGGGGGT 1201 CAAAGATGAG TGTTTTAGTG TATTCTTTCG CCTCTTTCGT TTTAGGTTGG TGCCTTCGTA 1261 GTGGCATTAC GTATTTTACC CGTTTAATGG AAACTTCCTC ATGAAAAAGT CTTTAGTCCT 1321 CAAAGCCTCT GTAGCCGTTG CTACCCTCGT TCCGATGCTG TCTTTCGCTG CTGAGGGTGA 1381 CGATCCCGCA AAAGCGGCCT TTAACTCCCT GCAAGCCTCA GCGACCGAAT ATATCGGTTA 1441 TGCGTGGGCG ATGGTTGTTG TCATTCTCGG CGCAACTATC GGTATCAAGC TGTTTAAGAA 1501 ATTCACCTCG AAAGCAAGCT GATAAACCGA TACAATTAAA GGCTCCTTTT GGAGCCTTTT 1561 TTTTTGGAGA TTTTCAACGT GAAAAAATTA TTATTCGCAA TTCCTTTAGT TGTTCCTTTC 1621 TATTCTCACA GTGCACAGTC TGTCGTGACG CAGCCGCCCT CAGTGTCTGG GGCCCCAGGG 1681 CAGAGGGTCA CCATCTCCTG CACTGGGAGC AGCTCCAACA TCGGGGCAGG TTATGATGTA 1741 CACTGGTACC AGCAGCTTCC AGGAACAGCC CCCAAACTCC TCATCTATGG TAACAGCAAT 1801 CGGCCCTCAG GGGTCCCTGA CCGATTCTCT GGCTCCAAGT CTGGCACCTC AGCCTCCCTG 1861 GCCATCACTG GGCTCCAGGC TGAGGATGAG GCTGATTATT ACTGCCAGTC CTATGACAGC 1921 AGCCTGAGTG GCCTTTATGT CTTCGGAACT GGGACCAAGG TCACCGTCCT AGGTCAGCCC 1981 AAGGCCAACC CCACTGTCAC TCTGTTCCCG CCCTCCTCTG AGGAGCTCCA AGCCAACAAG 2041 GCCACACTAG TGTGTCTGAT CAGTGACTTC TACCCGGGAG CTGTGACAGT GGCCTGGAAG 2101 GCAGATAGCA GCCCCGTCAA GGCGGGAGTG GAGACCACCA CACCCTCCAA ACAAAGCAAC 2161 AACAAGTACG CGGCCAGCAG CTATCTGAGC CTGACGCCTG AGCAGTGGAA GTCCCACAGA 2221 AGCTACAGCT GCCAGGTCAC GCATGAAGGG AGCACCGTGG AGAAGACAGT GGCCCCTACA 2281 GAATGTTCAT AATAAACCGC CTCCACCGGG CGCGCCAATT CTATTTCAAG GAGACAGTCA 2341 TAATGAAATA CCTATTGCCT ACGGCAGCCG CTGGATTGTT ATTACTCGCG GCCCAGCCGG 2401 CCATGGCCGA AGTTCAATTG TTAGAGTCTG GTGGCGGTCT TGTTCAGCCT GGTGGTTCTT 2461 TACGTCTTTC TTGCGCTGCT TCCGGATTCA CTTTCTCTTC GTACGCTATG TCTTGGGTTC 2521 GCCAAGCTCC TGGTAAAGGT TTGGAGTGGG TTTCTGCTAT CTCTGGTTCT GGTGGCAGTA 2581 CTTACTATGC TGACTCCGTT AAAGGTCGCT TCACTATCTC TAGAGACAAC TCTAAGAATA 2641 CTCTCTACTT GCAGATGAAC AGCTTAAGGG CTGAGGACAC TGCAGTCTAC TATTGCGCTA 2701 AAGACTATGA AGGTACTGGT TATGCTTTCG ACATATGGGG TCAAGGTACT ATGGTCACCG 2761 TCTCTAGTGC CTCCACCAAG GGCCCATCGG TCTTCCCCCT GGCACCCTCC TCCAAGAGCA 2821 CCTCTGGGGG CACAGCGGCC CTGGGCTGCC TGGTCAAGGA CTACTTCCCC GAACCGGTGA 2881 CGGTGTCGTG GAACTCAGGC GCCCTGACCA GCGGCGTCCA CACCTTCCCG GCTGTCCTAC 2941 AGTCTAGCGG ACTCTACTCC CTCAGCAGCG TAGTGACCGT GCCCTCTTCT AGCTTGGGCA 3001 CCCAGACCTA CATCTGCAAC GTGAATCACA AGCCCAGCAA CACCAAGGTG GACAAGAAAG 3061 TTGAGCCCAA ATCTTGTGCG GCCGCTCATC ACCACCATCA TCACTCTGCT GAACAAAAAC 3121 TCATCTCAGA AGAGGATCTG AATGGTGCCG CAGATATCAA CGATGATCGT ATGGCTGGCG 3181 CCGCTGAAAC TGTTGAAAGT TGTTTAGCAA AACCCCATAC AGAAAATTCA TTTACTAACG 3241 TCTGGAAAGA CGACAAAACT TTAGATCGTT ACGCTAACTA TGAGGGTTGT CTGTGGAATG 3301 CTACAGGCGT TGTAGTTTGT ACTGGTGACG AAACTCAGTG TTACGGTACA TGGGTTCCTA 3361 TTGGGCTTGC TATCCCTGAA AATGAGGGTG GTGGCTCTGA GGGTGGCGGT TCTGAGGGTG 3421 GCGGTTCTGA GGGTGGCGGT ACTAAACCTC CTGAGTACGG TGATACACCT ATTCCGGGCT 3481 ATACTTATAT CAACCCTCTC GACGGCACTT ATCCGCCTGG TACTGAGCAA AACCCCGCTA 3541 ATCCTAATCC TTCTCTTGAG GAGTCTCAGC CTCTTAATAC TTTCATGTTT CAGAATAATA 3601 GGTTCCGAAA TAGGCAGGGG GCATTAACTG TTTATACGGG CACTGTTACT CAAGGCACTG 3661 ACCCCGTTAA AACTTATTAC CAGTACACTC CTGTATCATC AAAAGCCATG TATGACGCTT 3721 ACTGGAACGG TAAATTCAGA GACTGCGCTT TCCATTCTGG CTTTAATGAA GATCCATTCG 3781 TTTGTGAATA TCAAGGCCAA TCGTCTGACC TGCCTCAACC TCCTGTCAAT GCTGGCGGCG 3841 GCTCTGGTGG TGGTTCTGGT GGCGGCTCTG AGGGTGGTGG CTCTGAGGGT GGCGGTTCTG 3901 AGGGTGGCGG CTCTGAGGGA GGCGGTTCCC GTGGTGGCTC TGGTTCCGGT GATTTTGATT 3961 ATGAAAAGAT GGCAAACGCT AATAAGGGGG CTATGACCGA AAATGCCGAT GAAAACGCGC 4021 TACAGTCTGA CGCTAAAGGC AAACTTGATT CTGTCGCTAC TGATTACGGT GCTGCTATCG 4081 ATGGTTTCAT TGGTGACGTT TCCGGCCTTG CTAATGGTAA TGGTGCTACT GGTGATTTTG 4141 CTGGCTCTAA TTCCCAAATG GCTCAAGTCG GTGACGGTGA TAATTCACCT TTAATGAATA 4201 ATTTCCGTCA ATATTTACCT TCCCTCCCTC AATCGGTTGA ATGTCGCCCT TTTGTCTTTA 4261 GCGCTGGTAA ACCATATGAA TTTTCTATTG ATTGTGACAA AATAAACTTA TTCCGTGGTG 4321 TCTTTGCGTT TCTTTTATAT GTTGCCACCT TTATGTATGT ATTTTCTACG TTTGCTAACA 4381 TACTGCGTAA TAAGGAGTCT TAATCATGCC AGTTCTTTTG GGTATTCCGT TATTATTGCG 4441 TTTCCTCGGT TTCCTTCTGG TAACTTTGTT CGGCTATCTG CTTACTTTTC TTAAAAAGGG 4501 CTTCGGTAAG ATAGCTATTG CTATTTCATT GTTTCTTGCT CTTATTATTG GGCTTAACTC 4561 AATTCTTGTG GGTTATCTCT CTGATATTAG CGCTCAATTA CCCTCTGACT TTGTTCAGGG 4621 TGTTCAGTTA ATTCTCCCGT CTAATGCGCT TCCCTGTTTT TATGTTATTC TCTCTGTAAA 4681 GGCTGCTATT TTCATTTTTG ACGTTAAACA AAAAATCGTT TCTTATTTGG ATTGGGATAA 4741 ATAATATGGC TGTTTATTTT GTAACTGGCA AATTAGGCTC TGGAAAGACG CTCGTTAGCG 4801 TTGGTAAGAT TCAGGATAAA ATTGTAGCTG GGTGCAAAAT AGCAACTAAT CTTGATTTAA 4861 GGCTTCAAAA CCTCCCGCAA GTCGGGAGGT TCGCTAAAAC GCCTCGCGTT CTTAGAATAC 4921 CGGATAAGCC TTCTATATCT GATTTGCTTG CTATTGGGCG CGGTAATGAT TCCTACGATG 4981 AAAATAAAAA CGGCTTGCTT GTTCTCGATG AGTGCGGTAC TTGGTTTAAT ACCCGTTCTT 5041 GGAATGATAA GGAAAGACAG CCGATTATTG ATTGGTTTCT ACATGCTCGT AAATTAGGAT 5101 GGGATATTAT TTTTCTTGTT CAGGACTTAT CTATTGTTGA TAAACAGGCG CGTTCTGCAT 5161 TAGCTGAACA TGTTGTTTAT TGTCGTCGTC TGGACAGAAT TACTTTACCT TTTGTCGGTA 5221 CTTTATATTC TCTTATTACT GGCTCGAAAA TGCCTCTGCC TAAATTACAT GTTGGCGTTG 5281 TTAAATATGG CGATTCTCAA TTAAGCCCTA CTGTTGAGCG TTGGCTTTAT ACTGGTAAGA 5341 ATTTGTATAA CGCATATGAT ACTAAACAGG CTTTTTCTAG TAATTATGAT TCCGGTGTTT 5401 ATTCTTATTT AACGCCTTAT TTATCACACG GTCGGTATTT CAAACCATTA AATTTAGGTC 5461 AGAAGATGAA ATTAACTAAA ATATATTTGA AAAAGTTTTC TCGCGTTCTT TGTCTTGCGA 5521 TTGGATTTGC ATCAGCATTT ACATATAGTT ATATAACCCA ACCTAAGCCG GAGGTTAAAA 5581 AGGTAGTCTC TCAGACCTAT GATTTTGATA AATTCACTAT TGACTCTTCT CAGCGTCTTA 5641 ATCTAAGCTA TCGCTATGTT TTCAAGGATT CTAAGGGAAA ATTAATTAAT AGCGACGATT 5701 TACAGAAGCA AGGTTATTCA CTCACATATA TTGATTTATG TACTGTTTCC ATTAAAAAAG 5761 GTAATTCAAA TGAAATTGTT AAATGTAATT AATTTTGTTT TCTTGATGTT TGTTTCATCA 5821 TCTTCTTTTG CTCAGGTAAT TGAAATGAAT AATTCGCCTC TGCGCGATTT TGTAACTTGG 5881 TATTCAAAGC AATCAGGCGA ATCCGTTATT GTTTCTCCCG ATGTAAAAGG TACTGTTACT 5941 GTATATTCAT CTGACGTTAA ACCTGAAAAT CTACGCAATT TCTTTATTTC TGTTTTACGT 6001 GCTAATAATT TTGATATGGT TGGTTCAATT CCTTCCATAA TTCAGAAGTA TAATCCAAAC 6061 AATCAGGATT ATATTGATGA ATTGCCATCA TCTGATAATC AGGAATATGA TGATAATTCC 6121 GCTCCTTCTG GTGGTTTCTT TGTTCCGCAA AATGATAATG TTACTCAAAC TTTTAAAATT 6181 AATAACGTTC GGGCAAAGGA TTTAATACGA GTTGTCGAAT TGTTTGTAAA GTCTAATACT 6241 TCTAAATCCT CAAATGTATT ATCTATTGAC GGCTCTAATC TATTAGTTGT TTCTGCACCT 6301 AAAGATATTT TAGATAACCT TCCTCAATTC CTTTCTACTG TTGATTTGCC AACTGACCAG 6361 ATATTGATTG AGGGTTTGAT ATTTGAGGTT CAGCAAGGTG ATGCTTTAGA TTTTTCATTT 6421 GCTGCTGGCT CTCAGCGTGG CACTGTTGCA GGCGGTGTTA ATACTGACCG CCTCACCTCT 6481 GTTTTATCTT CTGCTGGTGG TTCGTTCGGT ATTTTTAATG GCGATGTTTT AGGGCTATCA 6541 GTTCGCGCAT TAAAGACTAA TAGCCATTCA AAAATATTGT CTGTGCCACG TATTCTTACG 6601 CTTTCAGGTC AGAAGGGTTC TATCTCTGTT GGCCAGAATG TCCCTTTTAT TACTGGTCGT 6661 GTGACTGGTG AATCTGCCAA TGTAAATAAT CCATTTCAGA CGATTGAGCG TCAAAATGTA 6721 GGTATTTCCA TGAGCGTTTT TCCTGTTGCA ATGGCTGGCG GTAATATTGT TCTGGATATT 6781 ACCAGCAAGG CCGATAGTTT GAGTTCTTCT ACTCAGGCAA GTGATGTTAT TACTAATCAA 6841 AGAAGTATTG CTACAACGGT TAATTTGCGT GATGGACAGA CTCTTTTACT CGGTGGCCTC 6901 ACTGATTATA AAAACACTTC TCAAGATTCT GGCGTACCGT TCCTGTCTAA AATCCCTTTA 6961 ATCGGCCTCC TGTTTAGCTC CCGCTCTGAT TCCAACGAGG AAAGCACGTT ATACGTGCTC 7021 GTCAAAGCAA CCATAGTACG CGCCCTGTAG CGGCGCATTA AGCGCGGCGG GTGTGGTGGT 7081 TACGCGCAGC GTGACCGCTA CACTTGCCAG CGCCCTAGCG CCCGCTCCTT TCGCTTTCTT 7141 CCCTTCCTTT CTCGCCACGT TCGCCGGCTT TCCCCGTCAA GCTCTAAATC GGGGGCTCCC 7201 TTTAGGGTTC CGATTTAGTG CTTTACGGCA CCTCGACCCC AAAAAACTTG ATTTGGGTGA 7261 TGGTTCACGT AGTGGGCCAT CGCCCTGATA GACGGTTTTT CGCCCTTTGA CGTTGGAGTC 7321 CACGTTCTTT AATAGTGGAC TCTTGTTCCA AACTGGAACA ACACTCAACC CTATCTCGGG 7381 CTATTCTTTT GATTTATAAG GGATTTTGCC GATTTCGGAA CCACCATCAA ACAGGATTTT 7441 CGCCTGCTGG GGCAAACCAG CGTGGACCGC TTGCTGCAAC TCTCTCAGGG CCAGGCGGTG 7501 AAGGGCAATC AGCTGTTtCC CGTCTCACTG GTGAAAAGAA AAACCACCCT GGATCCAAGC 7561 TTGCAGGTGG CACTTTTCGG GGAAATGTGC GCGGAACCCC TATTTGTTTA TTTTTCTAAA 7621 TACATTCAAA TATGTATCCG CTCATGAGAC AATAACCCTG ATAAATGCTT CAATAATATT 7681 GAAAAAGGAA GAGTATGAGT ATTCAACATT TCCGTGTCGC CCTTATTCCC TTTTTTGCGG 7741 CATTTTGCCT TCCTGTTTTT GCTCACCCAG AAACGCTGGT GAAAGTAAAA GATGCTGAAG 7801 ATCAGTTGGG CGCACGAGTG GGTTACATCG AACTGGATCT CAACAGCGGT AAGATCCTTG 7861 AGAGTTTTCG CCCCGAAGAA CGTTTTCCAA TGATGAGCAC TTTTAAAGTT CTGCTATGTC 7921 ATACACTATT ATCCCGTATT GACGCCGGGC AAGAGCAACT CGGTCGCCGG GCGCGGTATT 7981 CTCAGAATGA CTTGGTTGAG TACTCACCAG TCACAGAAAA GCATCTTACG GATGGCATGA 8041 CAGTAAGAGA ATTATGCAGT GCTGCCATAA CCATGAGTGA TAACACTGCG GCCAACTTAC 8101 TTCTGACAAC GATCGGAGGA CCGAAGGAGC TAACCGCTTT TTTGCACAAC ATGGGGGATC 8161 ATGTAACTCG CCTTGATCGT TGGGAACCGG AGCTGAATGA AGCCATACCA AACGACGAGC 8221 GTGACACCAC GATGCCTGTA GCAATGCCAA CAACGTTGCG CAAACTATTA ACTGGCGAAC 8281 TACTTACTCT AGCTTCCCGG CAACAATTAA TAGACTGGAT GGAGGCGGAT AAAGTTGCAG 8341 GACCACTTCT GCGCTCGGCC CTTCCGGCTG GCTGGTTTAT TGCTGATAAA TCTGGAGCCG 8401 GTGAGCGTGG GTCTCGCGGT ATCATTGCAG CACTGGGGCC AGATGGTAAG CCCTCCCGTA 8461 TCGTAGTTAT CTACACGACG GGGAGTCAGG CAACTATGGA TGAACGAAAT AGACAGATCG 8521 CTGAGATAGG TGCCTCACTG ATTAAGCATT GGTAACTGTC AGACCAAGTT TACTCATATA 8581 TACTTTAGAT TGATTTAAAA CTTCATTTTT AATTTAAAAG GATCTAGGTG AAGATCCTTT 8641 TTGATAATCT CATGACCAAA ATCCCTTAAC GTGAGTTTTC GTTCCACTGT ACGTAAGACC 8701 CCCAAGCTTG TCGACTGAAT GGCGAATGGC GCTTTGCCTG GTTTCCGGCA CCAGAAGCGG 8761 TGCCGGAAAG CTGGCTGGAG TGCGATCTTC CTGAGGCCGA TACTGTCGTC GTCCCCTCAA 8821 ACTGGCAGAT GCACGGTTAC GATGCGCCCA TCTACACCAA CGTAACCTAT CCCATTACGG 8881 TCAATCCGCC GTTTGTTCCC ACGGAGAATC CGACGGGTTG TTACTCGCTC ACATTTAATG 8941 TTGATGAAAG CTGGCTACAG GAAGGCCAGA CGCGAATTAT TTTTGATGGC GTTCCTATTG 9001 GTTAAAAAAT GAGCTGATTT AACAAAAATT TAACGCGAAT TTTAACAAAA TATTAACGTT 9061 TACAATTTAA ATATTTGCTT ATACAATCTT CCTGTTTTTG GGGCTTTTCT GATTATCAAC 9121 CGGGGTACAT ATGATTGACA TGCTAGTTTT ACGATTACCG TTCATCGATT CTCTTGTTTG 9181 CTCCAGACTC TCAGGCAATG ACCTGATAGC CTTTGTAGAT CTCTCAAAAA TAGCTACCCT 9241 CTCCGGCATG AATTTATCAG CTAGAACGGT TGAATATCAT ATTGATGGTG ATTTGACTGT 9301 CTCCGGCCTT TCTCACCCTT TTGAATCTTT ACCTACACAT TACTCAGGCA TTGCATTTAA 9361 AATATATGAG GGTTCTAAAA ATTTTTATCC TTGCGTTGAA ATAAAGGCTT CTCCCGCAAA 9421 AGTATTACAG GGTCATAATG TTTTTGGTAC AACCGATTTA GCTTTATGCT CTGAGGCTTT 9481 ATTGCTTAAT TTTGCTAATT CTTTGCCTTG CCTGTATGAT TTATTGGATG TT

[0159] TABLE 200 Enzymes that either cut 15 or more human GLGs or have 5 + -base recognition in FR3 Typical entry: REname Recognition #sites GLGid#:base# GLGid#:base# GLGid#:base# BstEII Ggtnacc 2  1:  3   48:  3 There are 2 hits at base# 3 MaeIII gtnac 36  1:  4    2:  4    3:  4    4:  4    5:  4    6:  4  7:  4    8:  4    9:  4   10:  4   11:  4   37:  4 37: 58   38:  4   38: 58   39:  4   39: 58   40:  4 40: 58   41:  4   41: 58   42:  4   42: 58   43:  4 43: 58   44:  4   44: 58   45:  4   45: 58   46:  4 46: 58   47:  4   47: 58   48:  4   49:  4   50: 58 There are 24 hits at base# 4 Tsp45I gtsac 33  1:  4    2:  4    3:  4    4:  4    5:  4    6:  4  7:  4    8:  4    9:  4   10:  4   11:  4   37:  4  7: 58   38:  4   38: 58   39: 58   40:  4   40: 58 41: 58   42: 58   43:  4   43: 58   44:  4   44: 58 45:  4   45: 58   46:  4   46: 58   47:  4   47: 58 48:  4   49:  4   50: 58 There are 21 hits at base# 4 1-IphI tcacc 45  1:  5    2:  5    3:  5    4:  5    5:  5    6:  5  7:  5    8:  5   11:  5   12:  5   12: 11   13:  5 14:  5   15:  5   16:  5   17:  5   18:  5   19:  5 20:  5   21:  5   22:  5   23:  5   24:  5   25:  5 26:  5   27:  5   28:  5   29:  5   30:  5   31:  5 32:  5   33:  5   34:  5   35:  5   36:  5   37:  5 38:  5   40:  5   43:  5   44:  5   45:  5   46:  5 47:  5   48:  5   49:  5 There are 44 hits at base# 5 NlaIII CATG 26  1:  9    1: 42    2: 42    3:  9    3: 42    4:  9  4: 42    5:  9    5: 42    6: 42    6: 78    7:  9  7: 42    8: 21    8: 42    9: 42   10: 42   11: 42 12: 57   13: 48   13: 57   14: 57   31: 72   38:  9 48: 78   49: 78 There are 11 hits at base# 42 There are 1 hits at base# 48 Could cause raggedness. BsaJI Ccnngg 37  1: 14    2: 14    5: 14    6: 14    7: 14    8: 14  8: 65    9: 14   10: 14   11: 14   12: 14   13: 14 14: 14   15: 65   17: 14   17: 65   18: 65   19: 65 20: 65   21: 65   22: 65   26: 65   29: 65   30: 65 33: 65   34: 65   35: 65   37: 65   38: 65   39: 65 40: 65   42: 65   43: 65   48: 65   49: 65   50: 65 51: 14 There are 23 hits at base# 65 There are 14 hits at base# 14 AluI AGct 42  1: 47    2: 47    3: 47    4: 47    5: 47    6: 47  7: 47    8: 47    9: 47   10: 47   11: 47   16: 63 23: 63   24: 63   25: 63   31: 63   32: 63   36: 63 37: 47   37: 52   38: 47   38: 52   39: 47   39: 52 40: 47   40: 52   41: 47   41: 52   42: 47   42: 52 43: 47   43: 52   44: 47   44: 52   45: 47   45: 52 46: 47   46: 52   47: 47   47: 52   49: 15   50: 47 There are 23 hits at base# 47 There are 11 hits at base# 52 Only 5 bases from 47 BlpI GCtnagc 21  1: 48    2: 48    3: 48    5:48    6:48    7:48  8: 48    9: 48   10: 48   11:48   37:48   38:48 39: 48   40: 48   41: 48   42:48   43:48   44:48 45: 48   46: 48   47: 48 There are 21 hits at base# 48 MwoI GCNNNNNnngc 19  1: 48    2: 28   19: 36   22: 36   23: 36   24: 36 25: 36   26: 36   35: 36   37: 67   39: 67   40: 67 41: 67   42: 67   43: 67   44: 67   45: 67   46: 67 47: 67 There are 10 hits at base# 67 There are 7 hits at base# 36 DdeI Ctnag 71  1: 49    1: 58    2: 49    2: 58    3: 49    3: 58  3: 65    4: 49    4: 58    5: 49    5: 58    5: 65  6: 49    6: 58    6: 65    7: 49    7: 58    7: 65  8: 49    8: 58    9: 49    9: 58    9: 65   10: 49 10: 58   10: 65   11: 49   11: 58   11: 65   15: 58 16: 58   16: 65   17: 58   18: 58   20: 58   21: 58 22: 58   23: 58   23: 65   24: 58   24: 65   25: 58    25: 65   26: 58   27: 58   27: 65   28: 58   30: 58 31: 58   31: 65   32: 58   32: 65   35: 58   36: 58    36: 65   37: 49   38: 49   39: 26   39: 49   40: 49 41: 49   42: 26   42: 49   43: 49   44: 49   45: 49 46: 49   47: 49   48: 12   49: 12   51: 65 There are 29 hits at base# 58 There are 22 hits at base# 49 Only nine base from 58 There are 16 hits at base# 65 Only seven bases from 58 BglII Agatct 11  1: 61    2: 61    3: 61    4: 61    5: 61    6: 61  7: 61    9: 61   10: 61   11: 61   51: 47 There are 10 hits at base# 61 BstYI Rgatcy 12  1: 61    2: 61    3: 61    4: 61    5: 61    6: 61  7: 61    8: 61    9: 61   10: 61   11: 61   51: 47 There are 11 hits at base# 61 Hpy188I TCNga 17  1: 64    2: 64    3: 64    4: 64    5: 64    6: 64  7: 64    8: 64    9: 64   10: 64   11: 64   16: 57 20: 57   27: 57   35: 57   48: 67   49: 67 There are 11 hits at base# 64 There are 4 hits at base# 57 There are 2 hits at base# 67 Could be ragged. MslI CAYNNnnRTG 44  1: 72    2: 72    3: 72    4: 72    5: 72    6: 72  7: 72    8: 72    9: 72   10: 72   11: 72   15: 72 17: 72   18: 72   19: 72   21: 72   23: 72   24: 72 25: 72   26: 72   28: 72   29: 72   30: 72   31: 72 32: 72   33: 72   34: 72   35: 72   36: 72   37: 72 39: 72   39: 72   40: 72   41: 72   42: 72   43: 72 44: 72   45: 72   46: 72   47: 72   48: 72   49: 72 50: 72   51: 72 There are 44 hits at base# 72 BsiEI CGRYcg 23  1: 74    3: 74    4: 74    5: 74    7: 74    8: 74  9: 74   10: 74   11: 74   17: 74   22: 74   30: 74 33: 74   34: 74   37: 74   38: 74   39: 74   40: 74 41: 74   42: 74   45: 74   46: 74   47: 74 There are 23 hits at base# 74 EaeI Yggccr 23  1: 74    3: 74    4: 74    5: 74    7: 74    8: 74  9: 74   10: 74   11: 74   17: 74   22: 74   30: 74 33: 74   34: 74   37: 74   38: 74   39: 74   40: 74 41: 74   42: 74   45: 74   46: 74   47: 74 There are 23 hits at basef 74 EagI Cggccg 23  1: 74    3: 74    4: 74    5: 74    7: 74    8: 74  9: 74   10: 74   11: 74   17: 74   22: 74   30: 74 33: 74   34: 74   37: 74   38: 74   39: 74   40: 74 41: 74   42: 74   45: 74   46: 74   47: 74 There are 23 hits at base# 74 HaeIII GGcc 27  1: 75    3: 75    4: 75    5: 75    7: 75    8: 75  9: 75   10: 75   11: 75   16: 75   17: 75   20: 75 22: 75   30: 75   33: 75   34: 75   37: 75   38: 75 39: 75   40: 75   41: 75   42: 75   45: 75   46: 75 47: 75   48: 63   49: 63 There are 25 hits at base# 75 Bst4CI ACNgt 65° C. 63 Sites There is a third isoschismer  1: 86    2: 86    3: 86    4: 86    5: 86    6: 86  7: 34    7: 86    8: 86    9: 86   10: 86   11: 86 12: 86   13: 86   14: 96   15: 36   15: 86   16: 53 16: 86   17: 36   17: 86   18: 86   19: 86   20: 53 20: 86   21: 36   21: 86   22:  0   22: 66   23: 86 24: 86   25: 86   26: 86   27: 53   27: 86   28: 36 28: 86   29: 86   30: 86   31: 86   32: 86   33: 36 33: 86   34: 86   35: 53   35: 86   36: 86   37: 86 38: 86   39: 86   40: 86   41: 86   42: 86   43: 86 44: 86   45: 86   46: 86   47: 86   48: 86   49: 86 50: 86   51:  0   51: 86 There are 51 hits at base# 86 All the other sites are well away HpyCH4III ACNgt 63  1: 86    2: 86    3: 86    4: 86    5: 86    6: 86  7: 34    7: 86    8: 86    9: 86   10: 86   11: 86 12: 86   13: 86   14: 86   15: 36   15: 86   16: 53 16: 86   17: 36   17: 86   18: 86   19: 86   20: 53 20: 86   21: 36   21: 86   22:  0   22: 86   23: 86 24: 86   25: 86   26: 86   27: 53   27: 86   28: 36 28: 86   29: 86   30: 86   31: 86   32: 86   33: 36 33: 86   34: 86   35: 53   35: 86   36: 86   37: 86 38: 86   39: 86   40: 86   41: 86   42: 86   43: 86 44: 96   45: 86   46: 86   47: 86   48: 86   49: 86 50: 66   51:  0   51: 96 There are 51 hits at base# 86 Hinf I Gantc 43  2:  2    3:  2    4:  2    5:  2    6:  2    7: 2  8:  2    9:  2    9: 22   10:  2   11:  2   15: 2 16:  2   17:  2   19:  2   19:  2   19: 22   20: 2 21:  2   23:  2   24:  2   25:  2   26:  2   27: 2 28:  2   29:  2   30:  2   31:  2   32:  2   33: 2 33: 22   34: 22   35:  2   36:  2   37:  2   38: 2 40:  2   43:  2   44:  2   45:  2   46:  2   47: 2 50: 60 There are 38 hits at base# 2 MlyI GAGTCNNNNNn 18  2:  2    3:  2    4:  2    5:  2    6:  2    7:  2  8:  2    9:  2   10:  2   11:  2   37:  2   38:  2 40:  2   43:  2   44:  2   45:  2   46:  2   47:  2 There are 18 hits at base# 2 PleI gagtc 18  2:  2    3:  2    4:  2    5:  2    6:  2    7:  2  8:  2    9:  2   10:  2   11:  2   37:  2   38:  2 40:  2   43:  2   44:  2   45:  2   46:  2   47:  2 There are 18 hits at base# 2 AciI Ccgc 24  2: 26    9: 14   10: 14   11: 14   27: 74   37: 62 37: 65   38: 62   39: 65   40: 62   40: 65   41: 65 42: 65   43: 62   43: 65   44: 62   44: 65   45: 62 46: 62   47: 62   47: 65   48: 35   48: 74   49: 74 There are 8 hits at base# 62 There are 8 hits at base# 65 There are 3 hits at base# 14 There are 3 hits at base# 74 There are 1 hits at base# 26 There are 1 hits at base# 35 -″- Gcgg 11  8: 91    9: 16   10: 16   11: 16   37: 67   39: 67 40: 67   42: 67   43: 67   45: 67   46: 67 There are 7 hits at base# 67 There are 3 hits at base#16 There are 1 hits at base#91 BsiIHKAI GWGCWc 20  2: 30    4: 30    6: 30    7: 30    9: 30   10: 30 12: 89   13: 89   14: 89   37: 51   38: 51   39: 51 40: 51   41: 51   42: 51   43: 51   44: 51   45: 51 46: 51   47: 51 There are 11 hits at base# 51 Bsp1286I GDGCHc 20  2: 30    4: 30    6: 30    7: 30    9: 30   10: 30 12: 89   13: 89   14: 89   37: 51   38: 51   39: 51 40: 51   41: 51   42: 51   43: 51   44: 51   45: 51 46: 51   47: 51 There are 11 hits at base# 51 HgiAI GWGCWc 20  2: 30    4: 30    6: 30    7: 30    9: 30   10: 30 12: 89   13: 89   14: 89   37: 51   38: 51   39: 51 40: 51   41: 51   42: 51   43: 51   44: 51   45: 51 46: 51   47: 51 There are 11 hits at base# 51 BsoFI GCngc 26  2: 53    3: 53    5: 53    6: 53    7: 53    8: 53  8: 91    9: 53   10: 53   11: 53   31: 53   36: 36 37: 64   39: 64   40: 64   41: 64   42: 64   43: 64 44: 64   45: 64   46: 64   47: 64   48: 53   49: 53 50: 45   51: 53 There are 13 hits at base# 53 There are 10 hits at base# 64 TseI Gcwgc 17  2: 53    3: 53    5: 53    6: 53    7: 53    8: 53  9: 53   10: 53   11: 53   31: 53   36: 36   45: 64 46: 64   48: 53   49: 53   50: 45   51: 53 There are 13 hits at base# 53 MnlI gagg 34  3: 67    3: 95    4: 51    5: 16    5: 67    6: 67  7: 67    8: 67    9: 67   10: 67   11: 67   15: 67 16: 67   17: 67   19: 67   20: 67   21: 67   22: 67 23: 67   24: 67   25: 67   26: 67   27: 67   28: 67 29: 67   30: 67   31: 67   32: 67   33: 67   34: 67 35: 67   36: 67   50: 67   51: 67 There are 31 hits at base#67 HpyCH4V TGCa 34  5: 90    6: 90   11: 90   12: 90   13: 90   14: 90 15: 44   16: 44   16: 90   17: 44   16: 90   19: 44 20: 44   21: 44   22: 44   23: 44   24: 44   25: 44 26: 44   27: 44   27: 90   28: 44   29: 44   33: 44 34: 44   35: 44   35: 90   36: 39   48: 44   49: 44 50: 44   50: 90   51: 44   51: 52 There are 21 hits at base# 44 There are 1 hits at base# 52 AccI GTmkac 13 5-base recognition  7: 37   11: 24   37: 16   38: 16   39: 16   40: 16 41: 16   42: 16   43: 16   44: 16   45: 16   46: 16 47: 16 There are 11 hits at base# 16 SacII CCGCgg 8 6-base recognition  9: 14   10: 14   11: 14   37: 65   39: 65   40: 65 42: 65   43: 65 There are 5 hits at base# 65 There are 3 hits at base# 14 TfiI Gawtc 24  9: 22   15:  2   16:  2   17:  2   18:  2   19:  2 19: 22   20:  2   21:  2   23:  2   24:  2   25:  2 26:  2   27:  2   28:  2   29:  2   30:  2   31:  2 32:  2   33:  2   33: 22   34: 22   35:  2   36:  2 There are 20 hits at base# 2 BsmAI Nnnnnngagac 19 15: 12   16: 11   20: 11   21: 11   22: 11   23: 11 24: 11   25: 11   26: 11   27: 11   28: 12   28: 56 30: 11   31: 11   32: 11   35: 11   36: 11   44: 87 48: 87 There are 16 hits at base# 11 BpmI ctccag 19 15: 12   16: 12   17: 12   18: 12   20: 12   21: 12 22: 12   23: 12   24: 12   25: 12   26: 12   27: 12 28: 12   30: 12   31: 12   32: 12   34: 12   35: 12 36: 12 There are 19 hits at base# 12 XmnI GAANNnnttc 12 37: 30   38: 30   39: 30   40: 30   41: 30   42: 30 43: 30   44: 30   45: 30   46: 30   47: 30   50: 30 There are 12 hits at base# 30 BsrI NCcagt 12 37: 32   38: 32   39: 32   40: 32   41: 32   42: 32 43: 32   44: 32   45: 32   46: 32   47: 32   50: 32 There are 12 hits at base# 32 BanII GRGCYc 11 37: 51   38: 51   39: 51   40: 51   41: 51   42: 51 43: 51   44: 51   45: 51   46: 51   47: 51 There are 11 hits at base# 51 Ecl136I GAGctc 11 37: 51   38: 51   39: 51   40: 51   41: 51   42: 51 43: 51   44: 51   45: 51   46: 51   47: 51 There are 11 hits at base# 51 SacI GAGCTc 11 37: 51   38: 51   39: 51   40: 51   41: 51   42: 51 43: 51   44: 51   45: 51   46: 51   47: 51 There are 11 hits at base# 51

[0160] TABLE 206 ! Synthetic 3-23 FR3 of human heavy chains showning positions of possible cleavage sites ! Sites engineered into the synthetic gene are shown in upper case DNA ! with the RE name between vertical bars (as in Xibal I). ! RERSs frequently found in GLGs are shown below the synthetic sequence ! with the name to the right (as in gtn ac=MaeIII(24), indicating that ! 24 of the 51 GLGs contain the site) !                                                              |---FR3--- !                                                                89  90 (codon # in !                                                                 R   F  synthetic 3-23)                                                                      |cgc|ttc|  6 ! Allowed DNA                                                        |cgn|tty| !                                                                    |agr| !                                                                      ga ntc = HinfI (38) !                                                                      ga gtc = PleI (18) !                                                                      ga wtc = TfiI (20) !                                                                         gtn ac = MaeIII (24) !                                                                         gts ac = Tsp45I (21) !                                                                          tc acc = HphI (44) !       --------FR3------------------------------------------------- !          91  92  93  94  95  96  97  98  99  100  101  102  103  104  105 !          T   I   S   R   D   N   S   K   N   T   L   Y   L   Q   M          |act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|  51 !allowed|acn|ath|tcn|cgn|gay|aay|tcn|aar|aay|acn|ttr|tay|ttr|car|atg| !              |agy|agr|       |agy|            |ctn|   |ctn| !              |     ga|gac = BsmAI (16)                      ag ct = AluI (23) !             c|tcc ag = BpmI (19)                                g ctn agc = BlpI (21) !              |       |               g aan nnn ttc = XmnI (12) !              |XbaI  |                                  tg ca = HpyCH4V (21) ! !         ---FR3----------------------------------------------------->| !          106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !           N   S   L   R   A   E   D   T   A   V   Y   Y   C   A   K          |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgc|gct|aaa|  96 !allowed|aay|tcn|ttr|cgn|gcn|gar|gay|acn|gcn|gtn|tay|tay|tgy|gcn|aar| !           |agy|ctn|agr|             |       | !               |      |   cc nng g = BsaJI (23)        ac ngt = Bst4cI (51) !               |     aga tct = BglII (10)     |        ac ngt = HpyCH4III (51) !               |     Rga tcY = BstYI (11)     |        ac ngt = TaaI (51) !               |      |            c ayn nnn rtc = MslI (44) !               |      |               cg ryc g = BsiEI (23) !               |      |               yg gcc r = EaeI (23) !               |      |               cg gcc g = EagI (23) !               |      |               |g gcc = HaeIII (25) !               |      |      gag g = MnlI (31)| !               |AflII |               |PstI |

[0161] TABLE 217 Human HG GLG FR1 Sequences VH Exon-Nucleotide sequence alignment VH1 1-02 CAG GTG CAG CTG GTG CAG TCT GGG GCT GAG GTG AAG AAG CCT GGG GCC TCA GTG AAG GTC TCC TGC AAG GCT TCT GGA TAC ACC TTC ACC 1-03 cag gtC cag ctT gtg cag tct ggg gct gag gtg aag aag cct ggg gcc tca gtg aag gtT tcc tgc aag gct tct gga tac acc ttc acT 1-08 cag gtg cag ctg gtg cag tct ggg gct gag gtg aag aag cct ggg gcc tca gtg aag gtc tcc tgc aag gct tct gga tac acc ttc acc 1-18 cag gtT cag ctg gtg cag tct ggA gct gag gtg aag cag cct ggg gcc tca gtg aag gtc tcc tgc aag gct tct ggT tac acc ttT acc 1-24 cag gtC cag ctg gtA cag tct ggg gct gag gtg aag aag cct ggg gcc tca gtg aag gtc tcc tgc aag gTt tcC gga tac acc Ctc acT 1-45 cag Atg cag ctg gtg cag tct ggg gct gag gtg aag aag Act ggg Tcc tca gtg aag gtT tcc tgc aag gct tcC gga tac acc ttc acc 1-46 cag gtg cag ctg gtg cag tct ggg gct gag gtg aag aag cct ggg gcc tca gtg aag gtT tcc tgc aag gcA tct gga tac acc ttc acc 1-58 caA Atg cag ctg gtg cag tct ggg cct gag gtg aag aag cct ggg Acc tca gtg aag gtc tcc tgc aag gct tct gga tTc acc ttT acT 1-69 cag gtg cag ctg gtg cag tct ggg gct gag gtg aag aag cct ggg Tcc tcG gtg aag gtc tcc tgc aag gct tct gga GGc acc ttc aGc 1-e cag gtg cag ctg gtg cag tct ggg gct gag gtg aag aag cct ggg Tcc tcG gtg aag gtc tcc tgc aag gct tct gga GGc acc ttc aGc 1-f Gag gtC cag ctg gtA cag tct ggg gct gag gtg aag aag cct ggg gcT Aca gtg aaA Atc tcc tgc aag gTt tct gga tac acc ttc acc VH2 2-05 CAG ATC ACC TTG AAG GAG TCT GGT CCT ACG CTG GTG AAA CCC ACA CAG ACC CTC ACG CTG ACC TGC ACC TTC TCT GGG TTC TCA CTC AGC 2-26 cag Gtc acc ttg aag gag tct ggt cct GTg ctg gtg aaa ccc aca Gag acc ctc acg ctg acc tgc acc Gtc tct ggg ttc tca ctc agc 2-70 cag Gtc acc ttg aag gag tct ggt cct Gcg ctg gtg aaa ccc aca cag acc ctc acA ctg acc tgc acc ttc tct ggg ttc tca ctc agc VH3 3-07 GAG GTG CAG CTC GTG GAG TCT GGG GGA GGC TTG GTC CAG CCT GGG GGG TCC CTG AGA CTC TCC TGT GCA GCC TCT GGA TTC ACC TTT AGT 3-09 gaA gtg cag ctg gtg gag tct ggg gga ggc ttg gtA cag cct ggC Agg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttt GAt 3-11 Cag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc Aag cct ggA ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttC agt 3-13 gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtA cag cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttC agt 3-15 gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtA Aag cct ggg ggg tcc ctT aga ctc tcc tgt gca gcc tct gga ttc acT ttC agt 3-20 gag gtg cag ctg gtg gag tct ggg gga ggT Gtg gtA cGg cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttt GAt 3-21 gag gtg cag ctg gtg gag tct ggg gga ggc Gtg gtc Aag cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttC agt 3-23 gag gtg cag ctg Ttg gag tct ggg gga ggc ttg gtA cag cct ggg ggg tac ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttt agC 3-30 Cag gtg cag ctg gtg gag tct ggg gga ggc Gtg gtc cag cct ggg Agg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttc agt 3-30.3 Cag gtg cag ctg gtg gag tct ggg gga ggc Gtg gtc cag cct ggg Agg tcc ctg aga ctc tcc tgt gca gcc tct gga ttC acc ttG agt 3-30.5 Cag gtg cag ctg gtg gag tct ggg gga ggc Gtg gtc cag cct ggg Agg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttC agt 3-33 Cag gtg cag ctg gtg gag tct ggg gga ggc Gtg gtc cag cct ggg Agg tcc ctg aga ctc tcc tgt gca gcG tct gga ttc acc ttC agt 3-43 gaA gtg cag ctg gtg gag tct ggg gga gTc Gtg gtA cag cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttt GAt 3-48 gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtA cag cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttc agt 3-49 gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtA cag ccA ggg Cgg tcc ctg aga ctc tcc tgt Aca gcT tct qga ttc acc ttt Ggt 3-53 gag gtg cag ctg gtg gag Act ggA gga ggc ttg Atc cag cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct ggG ttc acc GtG agt 3-64 gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc cag cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttG agt 3-66 gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc cag cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc GtC agt 3-72 gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc cag cct ggA ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttC agt 3-73 gag gtg cag ctg gtg gag tct ggg gga ggc ttg gtc cag cct ggg ggg tcc ctg aAa ctc tcc tgt gca gcc tct ggG ttc acc ttc agt 3-74 gag gtg cag ctg gtg gag tcC ggg gga ggc ttA gtT cag cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc ttG agt 3-d gag gtg cag ctg gtg gag tct Cgg gga gTc ttg gtA cag cct ggg ggg tcc ctg aga ctc tcc tgt gca gcc tct gga ttc acc GtC agt VH4 4-04 GAG GTG GAG CTG GAG GAG TGG CCC GGA CGA CTG GTG AAG CCT TCG GGG ACC CTG TCC CTC AGC TGC GGT GTC TCT GGT CCC TCC ATC AGC 4-28 cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAG acc ctg tcc ctc acc tgc gct gtc tct ggt TAc tcc atc agc 4-30.1 cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcA GAg acc ctg tcc ctc acc tgc Act gtc tct ggt ggc tcc atc agc 4-30.2 cag Ctg cag ctg cag gag tcG ggc Tca gga ctg gtg aag cct tcA GAg acc ctg tcc ctc acc tgc gct gtc tct ggt ggc tcc atc agc 4-30.4 cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcA GAg acc ctg tcc ctc acc tgc Act gtc tct ggt ggc tcc atc agc 4-31 cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcA CAg acc ctg tcc ctc acc tgc Act gtc tct ggt ggc tcc atc agc 4-34 cag gtg cag ctA cag Cag tGg ggc Gca gga ctg Ttg aag cct tcg gAg acc ctg tcc ctc acc tgc gct gtc tAt ggt ggG tcc Ttc agT 4-39 cag Ctg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAg acc ctg tcc ctc acc tgc Act gtc tct ggt ggc tcc atc agc 4-59 cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAg acc ctg tcc ctc acc tgc Act gtc tct ggt ggc tcc atc agT 4-61 cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAg acc ctg tcc ctc acc tgc Act gtc tct ggt ggc tcc Gtc agc 4-b cag gtg cag ctg cag gag tcg ggc cca gga ctg gtg aag cct tcg gAg acc ctg tcc ctc acc tgc gct gtc tct ggt TAc tcc atc agc VH5 5-51 GAG GTG CAG CTG GTG CAG TCT GGA GCA GAG GTG AAA AAG CCC GGG GAG TCT CTG AAG ATC TCC TGT AAG GGT TCT GGA TAC AGC TTT ACC 5-a gaA gtg cag ctg gtg cag tct gga gca gag gtg aaa aag ccc ggg gag tct ctg aGg atc tcc tgt aag ggt tct gga tac agc ttt acc VH6 6-1 CAG GTA CAG CTG CAG CAG TCA GCT CCA GGA CTG GTG AAG CCC TCG CAG ACC CTC TCA CTC ACC TGT GCC ATC TCC GGG GAC AGT GTC TCT VH7 7-4.1 CAG GTG CAG CTG GTG CAA TCT GGG TCT GAG TTG AAG AAG CCT GGG GCC TCA GTG AAG GTT TCC TGC AAG GCT TCT GGA TAC ACC TTC ACT

[0162] TABLE 220 RERS Sites in Human HC GLG FR1s where there are at least 20 GLGs cut Bsg1 GTGCAG                      71 (cuts 16 14 bases to right)  1:  4     1: 13     2: 13     3:  4     3:13     4: 13  6: 13     7:  4     7: 13     8: 13     9:  4     9: 13 10:  4   10: 13   15:  4   15: 65   16:  4   16: 65 27:  4   17: 65   18:  4   18: 65   19:  4   19: 65 20:  4   20: 65   21:  4   21: 65   22:  4   22: 65 23:  4   23: 65   24:  4   24: 65   25:  4   25: 65 26:  4   26: 65   27:  4   27: 65   28:  4   28: 65 29:  4   30:  4   30: 65   31:  4   31: 65   32:  4 32: 65   33:  4   33: 65   34:  4   34: 65   35:  4 35: 65   36:  4   36: 65   37:  4   38:  4   39:  4 41:  4   42:  4   43:  4   45:  4   46:  4   47:  4 48:  4   48: 13   49:  4   49: 13   51:  4 There are 39 hits at base# 4 There are 21 hits at base#65 -″- ctgcac                     9 12: 63   13: 63   14: 63   39: 63   41: 63   42: 63 44: 63   45: 63   46: 63 BbvI GCAGC                    65  1:  6     3:  6     6:  6     7:  6     8:  6     9:  6 10:  6   15:  6   15: 67   16:  6   16: 67   17:  6 17: 67   18:  6   18: 67   19:  6   19: 67   20:  6 20: 67   21:  6   21: 67   22:  6   22: 67   23:  6 23: 67   24:  6   24: 67   25:  6   25: 67   26:  6 26: 67   27:  6   27: 67   28:  6   28: 67   29:  6 30:  6   30: 67   31:  6   31: 67   32:  6   32: 67 33:  6   33: 67   34:  6   34: 67   35:  6   35: 67 36:  6   36: 67   37:  6   38:  6   39:  6   40:  6 41:  6   42:  6   43:  6   44:  6   45:  6   46:  6 47:  6   48:  6   49:  6   50: 12   51:  6 There are 43 hits at base#6 Bolded sites very near sites listed below There are 21 hits at base#67 -″- gctgc                    13 37:  9   38:  9   39:  9   40:  3   40:  9   41:  9 42:  9   44:  3   44:  9   45:  9   46:  9   47:  9 50:  9 There are 11 hits at base#9 BsoFI GCngc 78  1:  6    3:  6    6:  6    7:  6  8:  6    9:  6 10:  6   15:  6   15: 67   16:  6   16: 67   17:  6 17: 67   18:  6   18: 67   19:  6   19: 67   20:  6 20: 67   21:  6   21: 67   22:  6   22: 67   23:  6 23: 67   24:  6   24: 67   25:  6   25: 67   26:  6 26: 67   27:  6   27: 67   28:  6   28: 67   29:  6 30:  6   30: 67   31:  6   31: 67   32:  6   32: 67 33:  6   33: 67   34:  6   34: 67   35:  6   35: 67 36:  6   36: 67   37:  6   37:  9  38:  6   38:  9 39:  6   39:  9   40:  3   40:  6   40:  9  41:  6 41:  9   42:  6   42:  9   43:  6   44:  3   44:  6 44:  9  45:  6   45:  9  46:  6   46:  9  47:  6 47:  9  48:  6   49:  6   50:  9   50: 12   51:  6 There are 43 hits at base#6 These of ten occur together. There are 11 hits at base#9 There are 2 hits at base#3 There are 21 hits at base#67 TseI Gcwgc                    78  1:  6    3:  6    6:  6    7:  6    8:  6    9:  6 10:  6   15:  6   15: 67   16:  6   16: 67   17:  6 17: 67   18:  6   18: 67   19:  6   19: 67   20:  6 20: 67   21:  6   21: 67   22:  6   22: 67   23:  6 23: 67   24:  6   24: 67   25:  6   25: 67   26:  6 26: 67   27:  6   27: 67   28:  6   28: 67   29:  6 30:  6   30: 67   31:  6   31: 67   32:  6   32: 67 33:  6   33: 67   34:  6   34: 67   35:  6   35: 67 36:  6   36: 67   37:  6   37:  9  38:  6   38:  9 39:  6   39:  9  40:  3   40:  6   40:  90   41:  6 41:  9  42:  6   42:  9  43:  6   44:  3   44:  6 44:  9  45:  6   45:  9  46:  6   46:  9  47:  6 47:  9  48:  6   49:  6   50:  9   50: 12  51:  6 There are 43 hits at base#6 Often together. There are 11 hits at base#9 There are 2 hits at base#3 There are 1 hits at base#12 There are 21 hits at base#67 MspAlI CMGckg                    48  1:  7    3:  7    4:  7    5:  7    6:  7    7:  7  8:  7    9:  7   10:  7   11:  7   15:  7   16:  7 17:  7   18:  7   19:  7   20:  7   21:  7   22:  7 23:  7   24:  7   25:  7   26:  7   27:  7   28:  7 29:  7   30:  7   31:  7   32:  7   33:  7   34:  7 35:  7   36:  7   37:  7   38:  7   39:  7   40:  1 40:  7  41:  7   42:  7   44:  1   44:  7  45:  7 46:  7   47:  7   48:  7   49:  7   50:  7   51:  7 There are 46 hits at base#7 PvuII CAGctg                     48  1:  7    3:  7    4:  7    5:  7    6:  7   7:  7  8:  7    9:  7   10:  7   11:  7   15:  7   16:  7 17:  7   18:  7   19:  7   20:  7   21:  7   22:  7 23:  7   24:  7   25:  7   26:  7   27:  7   28:  7 29:  7   30:  7   31:  7   32:  7   33:  7   34:  7 35:  7   36:  7   37:  7   38:  7   39:  7   40:  1 40:  7  41:  7   42:  7   44:  1   44:  7  45:  7 46:  7   47:  7   48:  7   49:  7   50:  7   51:  7 There are 46 hits at base#7 There are 2 hits at base#1 AluI AGct                    54  1:  8    2:  8    3:  8    4:  8    4: 24    5:  8  6:  8    7:  8    8:  8    9:  8   10:  8 11:  8 15:  8   16:  8   17:  8   18:  8   19:  8   20:  8 21:  8   22:  8   23:  8   24:  8   25:  8   26:  8 27:  8   28:  8   29:  8   29: 69   30:  8   31:  8 32:  8   33:  8   34:  8   35:  8   36:  8   37:  8 38:  8   39:  8   40:  2   40:  8  41:  8   42:  8 43:  8   44:  2   44:  8  45:  8   46:  8   47:  8 48:  8   48: 82   49:  8   49: 82   50:  8   51:  8 There are 48 hits at base#8 There are 2 hits at base#2 DdeI Ctnag                    48  1: 26    1: 48    2: 26    2: 48    3: 26    3: 48  4: 26    4: 48    5: 26    5: 48    6: 26    6: 48  7: 26    7: 48    8: 26    8: 48    9: 26   10: 26 11: 26   12: 85   13: 85   14: 85   15: 52   16: 52 17: 52   18: 52   19: 52   20: 52   21: 52   22: 52 23: 52   24: 52   25: 52   26: 52   27: 52   28: 52 29: 52   30: 52   31: 52   32: 52   33: 52   35: 30 35: 52   36: 52   40: 24   49: 52   51: 26   51: 48 There are 22 hits at base#52 52 and 48 never together. There are 9 hits at base#48 There are 12 hits at base#26 26 and 24 never together. HphI tcacc                    42  1: 86    3: 86    6: 86    7: 86    8: 80 11: 86 12:  5   13:  5   14:  5   15: 80   16: 80   17: 80 18: 80   20: 80   21: 80   22: 80   23: 80   24: 80 25: 80   26: 80   27: 80   28: 80   29: 80   30: 80 31: 80   32: 80   33: 80   34: 80   35: 80   36: 80 37: 59   38: 59   39: 59   40: 59   41: 59   42: 59 43: 59   44: 59   45: 59   46: 59   47: 59   50: 59 There are 22 hits at base#80 80 and 86 never together There are 5 hits at base#86 There are 12 hits at base#59 BssKI Nccngg                    50  1: 39    2: 39    3: 39    4: 39    5: 39    7: 39  8: 39    9: 39   10: 39   11: 39   15: 39   16: 39 17: 39   18: 39   19: 39   20: 39   21: 29   21: 39 22: 39   23: 39   24: 39   25: 39   26: 39   27: 39 28: 39   29: 39   30: 39   31: 39   32: 39   33: 39 34: 39   35: 19   35: 39   36: 39   37: 24   38: 24 39: 24   41: 24   42: 24   44: 24   45: 24   46: 24 47: 24   48: 39   48: 40  49: 39   49: 40  50: 24 50: 73   51: 39 There are 35 hits at base#39 39 and 40 together twice. There are 2 hits at base#40 BsaJI Ccnngg                    47  1: 40    2: 40    3: 40    4: 40    5: 40    7: 40  8: 40    9: 40    9: 47   10: 40   10: 47   11: 40 15: 40   18: 40   19: 40   20: 40   21: 40   22: 40 23: 40   24: 40   25: 40   26: 40   27: 40   28: 40 29: 40   30: 40   31: 40   32: 40   34: 40   35: 20 35: 40   36: 40   37: 24   38: 24   39: 24   41: 24 42: 24   44: 24   45: 24   46: 24   47: 24   48: 40 48: 41  49: 40   49: 41  50: 74   51: 40 There are 32 hits at base#40 40 and 41 together twice There are 2 hits at base#41 There are 9 hits at base#24 There are 2 hits at base#47 BstNI Ccwgg                    44 PspGI ccwgg ScrFI ($M.HpaII) CCwgg  1: 40    2: 40    3: 40    4: 40    5: 40    7: 40  8: 40    9: 40   10: 40   11: 40   15: 40   16: 40 17: 40   18: 40   19: 40   20: 40   21: 30   21: 40 22: 40   23: 40   24: 40   25: 40   26: 40   27: 40 28: 40   29: 40   30: 40   31: 40   32: 40   33: 40 34: 40   35: 40   36: 40   37: 25   38: 25   39: 25 41: 25   42: 25   44: 25   45: 25   46: 25   47: 25 50: 25   51: 40 There are 33 hits at base#40 ScrFI CCngg                    50  1: 40    2: 40    3: 40    4: 40    5: 40    7: 40  8: 40    9: 40   10: 40   11: 40   15: 40   16: 40 17: 40   18: 40   19: 40   20: 40   21: 30   21: 40 22: 40   23: 40   24: 40   25: 40   26: 40   27: 40 28: 40   29: 40   30: 40   31: 40   32: 40   33: 40 34: 40   35: 20   35: 40   36: 40   37: 25   38: 25 39: 25   41: 25   42: 25   44: 25   45: 25   46: 25 47: 25   48: 40   48: 41   49: 40   49: 41   50: 25 50: 74   51: 40 There are 35 hits at base#40 There are 2 hits at base#41 Eco01091 RGgnccy                       34  1: 43    2: 43    3: 43    4: 43    5: 43    6: 43  7: 43    8: 43    9: 43   10: 43   15: 46   16: 46 17: 46   18: 46   19: 46   20: 46   21: 46   22: 46 23: 46   24: 46   25: 46   26: 46   27: 46   28: 46 30: 46   31: 46   32: 46   33: 46   34: 46   35: 46 36: 46   37: 46   43: 79   51: 43 There are 22 hits at base#46 46 and 43 never together There are 11 hits at base#43 NlaIV GGNncc                       71  1: 43    2: 43    3: 43    4: 43    5: 43    6: 43  7: 43    8: 43    9: 43    9: 79   10: 43   10: 79 15: 46   15: 47  16: 47   17: 46   17: 47  18: 46 18: 47  19: 46   19: 47  20: 46   20: 47  21: 46 21: 47  22: 46   22: 47  23: 47   24: 47   25: 47 26: 47   27: 46   27: 47  28: 46   28: 47  29: 47 30: 46   30: 47  31: 46   31: 47  32: 46   32: 47 33: 46   33: 47  34: 46   34: 47  35: 46   35: 47 36: 46   36: 47  37: 21   37: 46   37: 47  37: 79 38: 21   39: 21   39: 79   40: 79   41: 21   41: 79 42: 21   42: 79   43: 79   44: 21   44: 79   45: 21 45: 79   46: 21   46: 79   47: 21   51: 43 There are 23 hits at base#47 46 & 47 often together There are 17 hits at base#46 There are 11 hits at base#43 Sau96I Ggncc                    70  1: 44    2: 3     2: 44    3: 44    4: 44    5: 3    5: 44    6: 44  7: 44    8: 22    8: 44    9: 44  10: 44  11: 3   12: 22  13: 22 14: 22   15: 33   15: 47   16: 47   17: 47   18: 47   19: 47   20: 47 21: 47   22: 47   23: 33   23: 47   24: 33   24: 47   25: 33   25: 47 26: 33   26: 47   27: 47   28: 47   29: 47   30: 47   31: 33   31: 47 32: 33   32: 47   33: 33   33: 47   34: 33   34: 47   35: 47   36: 47 37: 21   37: 22  37: 47   38: 21   38: 22  39: 21   39: 22   41: 21 41: 22   42: 21   42: 22   43: 80   44: 21   44: 22   45: 21   45: 22 46: 21   46: 22   47: 21   47: 22   50: 22   51: 44 There are 23 hits at base#47 These do not occur together. There are 11 hits at base#44 There are 14 hits at base#22 These do occur together. There are 9 hits at base#21 BsmAI GTCTCNnnnn                        22  1: 58    3: 58    4: 58    5: 58    8: 58    9: 58 10: 58   13: 70   36: 18   37: 70   38: 70   39: 70 40: 70   41: 70   42: 70   44: 70   45: 70   46: 70 47: 70   48: 48   49: 48   50: 85 There are 11 hits at base#70 -″- Nnnnnngagac                    27 13: 40   15: 48   16: 48   17: 48   18: 48   20: 48 21: 48   22: 48   23: 48   24: 48   25: 48   26: 48 27: 48   28: 48   29: 48   30: 10   30: 48   31: 48 32: 48   33: 48   35: 48   36: 48   43: 40   44: 40 45: 40   46: 40   47: 40 There are 20 hits at base#48 AvaII Ggwcc                     44 Sau96I($M.HaeIII) Ggwcc         44  2: 3     5: 3     6: 44     8: 44     9: 44   10: 44 11: 3     12: 22   13: 22   14: 22   15: 33   15: 47 16: 47   17: 47   18: 47   19: 47   20: 47   21: 47 22: 47   23: 33   23: 47   24: 33   24: 47   25: 33 25: 47   26: 33   26: 47   27: 47   28: 47   29: 47 30: 47   31: 33   31: 47   32: 33   32: 47   33: 33 33: 47   34: 33   34: 47   35: 47   36: 47   37: 47 43: 80   50: 22 There are 23 hits at base#47 44 & 47 never together There are 4 hits at base#44 PpuMI RGgwccy                    27  6: 43     8: 43     9: 43   10: 43   15: 46   16: 46 17: 46   18: 46   19: 46   20: 46   21: 46   22: 46 23: 46   24: 46   25: 46   26: 46   27: 46   28: 46 30: 46   31: 46   32: 46   33: 46   34: 46   35: 46 36: 46   37: 46   43: 79 There are 22 hits at base#46 43 and 46 never occur together. There are 4 hits at base#43 BsmFI GGGAC                        3  8: 43   37: 46   50: 77 -″- gtccc                           33 15: 48   16: 48   17: 48     1: 0    1: 0     20: 48 21: 48   22: 48   23: 48   24: 48   25: 48   26: 48 27: 48   28: 48   29: 48   30: 48   31: 48   32: 48 33: 48   34: 48   35: 48   36: 48   37: 54   38: 54 39: 54   40: 54   41: 54   42: 54   43: 54   44: 54 45: 54   46: 54   47: 54 There are 20 hits at base#48 There are 11 hits at base#54 HinfI Ganto                      80  8: 77   12: 16   13: 16   14: 16   15: 16   15: 56 15: 77   16: 16   16: 56   16: 77   17: 16   17: 56 17: 77   18: 16   18: 56   18: 77   19: 16   19: 56 19: 77   20: 16   20: 56   20: 77   21: 16   21: 56 21: 77   22: 16   22: 56   22: 77   23: 16   23: 56 23: 77   24: 16   24: 56   24: 77   25: 16   25: 56 25: 77   26: 16   26: 56   26: 77   27: 16   27: 26 27: 56   27: 77   28: 16   28: 56   28: 77   29: 16 29: 56   29: 77   30: 56   31: 16   31: 56   31: 77 32: 16   32: 56   32: 77   33: 16   33: 56   33: 77 34: 16   35: 16   35: 56   35: 77   36: 16   36: 26 36: 56   36: 77   37: 16   38: 16   39: 16   40: 16 41: 16   42: 16   44: 16   45: 16   46: 16   47: 16 48: 46   49: 46 There are 34 hits at base#16 TfiI Gawtc                        21  8: 77   15: 77   16: 77   17: 77   18: 77   19: 77 20: 77   21: 77   22: 77   23: 77   24: 77   25: 77 26: 77   27: 77   28: 77   29: 77   31: 77   32: 77 33: 77   35: 77   36: 77 There are 21 hits at base#77 MlyI GAGTC                    38 12: 16   13: 16   14: 16   15: 16   16: 16   17: 16 18: 16   19: 16   20: 16   21: 16   22: 16   23: 16 24: 16   25: 16   26: 16   27: 16   27: 26   28: 16 29: 16   31: 16   32: 16   33: 16   34: 16   35: 16 36: 16   36: 26   37: 16   38: 16   39: 16   40: 16 41: 16   42: 16   44: 16   45: 16   46: 16   47: 16 48: 46   49: 46 There are 34 hits at base#16 -″- GACTC                        21 15: 56   16: 56   17: 56   18: 56   19: 56   20: 56 21: 56   22: 56   23: 56   24: 56   25: 56   26: 56 27: 56   28: 56   29: 56   30: 56   31: 56   32: 56 33: 56   35: 56   36: 56 There are 21 hits at base#56 PleI gagtc                           38 12: 16   13: 16   14: 16   15: 16   16: 16   17: 16 18: 16   19: 16   20: 16   21: 16   22: 16   23: 16 24: 16   25: 16   26: 16   27: 16   27: 26   28: 16 29: 16   31: 16   32: 16   33: 16   34: 16   35: 16 36: 16   36: 26   37: 16   38: 16   39: 16   40: 16 41: 16   42: 16   44: 16   45: 16   46: 16   47: 16 48: 46   49: 46 There are 34 hits at base#16 -″- gactc                    21 15: 56   16: 56   17: 56   18: 56   19: 56   20: 56 21: 56   22: 56   23: 56   24: 56   25: 56   26: 56 27: 56   28: 56   29: 56   30: 56   31: 56   32: 56 33: 56   35: 56   36: 56 There are 21 hits at base#56 AlwNI CAGNNNctg                    26 15: 68   16: 68   17: 68   18: 68   19: 68   20: 68 21: 68   22: 68   23: 68   24: 68   25: 68   26: 68 27: 68   28: 68   29: 68   30: 68   31: 68   32: 68 33: 68   34: 68   35: 68   36: 68   39: 46   40: 46 41: 46   42: 46 There are 22 hits at base#69

[0163] TABLE 255 Analysis of frequency of matching REdaptors in actual V genes A: HpyCH4V in HC at bases 35-56 Number of mismatches.....................Number Id Ntot 0 1 2 3 4 5 6 7 8 9 10 Cut Id Probe 1  510   5 11 274  92   61   25   22   11    1    3    5  443 6-1 agttctcccTGCAgctgaactc 2  192  54 42  32  24   15    2    3   10    3    1    6  167 3-11 cactqtatcTGCAaatgaacag 3   58  19 7  17   6    5    1    0    1    0    2    0   54 3-09 ccctgtatcTGCAaatgaacag 4  267  42 33   9   8    8   82   43   22    8   11 1  100 5-51 ccgcctaccTGCAgtggagcag 5  250 111 59  41  24    7    5    1    0    0    2    0  242 3-15 cgctgtatcTGCAaatgaaaag 6    7   0   2   0    1    0    0    0    0    0    4    0    3 7-4.1 cggcatatcTGCAgatctgcag 7    7   0   2   2    0    0    2    1    0    0    0    0    4 3-73 cggcgtatcTGCAaatgaacag 8   26  10   4   1    3    1    2    1    3    1    0    0   19 5-a ctgcctaccTGCAgtggagcag 9   21   8   2  3    1    6    1    0    0    0    0    0   20 3-49 tcgcctatcTGCAaatgaacag 1338  249 162 379 149  103  120   71   47   13   23   12 1052  249 411 790 939 1162 1280 1316 1042 1233 1293 1338+TZ,1 59 Id Probe dotted probe+TZ,1 59 6-1 agttctcccTGCAgctgaactc agttctcccTGCAgctgaactc 3-11 cactgtatcTGCAaatgaacag cac.g.at.....aa.....ag 3-09 ccctgtatcTGCAaatgaacag ccc.g.at.....aa.....ag 5-51 ccgcctaccTGCAgtggagcag ccgc..a.......tg..g.ag 3-15 cgctgtatcTGCAaatgaacag c.c.g.at.....aa.....ag 7-4.1 cggcatatcTGCAqatctgcag c.gca.at......a.ctg.ag 3-73 cggcgtatcTGCAaatgaacag c.gcg.at.....aa.....ag 5-a ctgcctaccTGCAgtggagcag ctgc..a.......tg..g.ag 3-49 tcgcctatcTGCAaatgaacag tcgc..at.....aa.....ag+TZ,1 59 Seqs with the expected RE site only.......1004 (Counts only cases with 4 or fewer mismatches) Seqs with only an unexpected site......... 0 Seqs with both expected and unexpected.... 48 (Counts only cases with 4 or fewer mismatches) Seqs with no sites........................ 0 B: BlpI in HC Id Ntot 0 1 2 3 4 5 6 7 8 Ncut Name /1 133 /73 /16 /11 /13 //6 //9 //1 //4 //0 119 1-58 acatggaGCTGAGCagactgag /2 /14 /11 //1 //0 //0 //0 //0 //1 //0 //1 //12 1-02 acatggagctgagcaggctgag /3 /34 /17 //8 // 2 //6 //1 //0 //0 //0 //0 //0 1-18 acatggagctgaggagcctgag /4 120 /50 /32 /16 /10 //9 //1 //1 //1 //0 //2 5-51 acctgcagtggagcagcctgaa /5 /55 /13 /11 /10 /17 //3 //1 //0 //0 //0 //0 3-15 atctgcaaatgaacagcctgaa /6 340 186 /88 /41 /15 //6 //3 //0 //1 //0 //0 3303 atctgcaaatgaacagcctgag /7 /82 /25 /16 /25 /12 //1 //3 //0 //0 //0 //0 3-20 atctgcaaatgaacagtctgag /8 //3 // 0 //2 //0 //1 //0 //0 //0 //0 //0 //0 74.1 atctgcagatctgcagcctaaa /9 /23 /18 //2 //2 //1 //0 //0 //0 //0 //0 //0 3-66 atcttcaaatgaacagcctgag 10 //2 //1 //0 //1 //0 //0 //0 //0 //0 //0 //0 3-64 atcttcaaatgggcagcctgag 11 486 249 /78 /81 /38 /21 /10 //4 //4 //1 467 4301 ccctgaagctgagctctgtgac 12 /16 //6 //3 //1 //0 //1 //1 //3 //1 //0 //1 6-1 ccctgcagctgaactctgtgac 13 /28 /15 //8 //2 //2 //1 //0 //0 //0 //0 //0 2-70 tccttacaatgaccaacatgga 14 //2 //0 //2 //0 //0 //0 //0 //0 //0 //0 //0 2-26 tccttaccatgaccaacatgga 601 Name Full sequence Dot mode 1-58 acatggaGCTGAGCagcctgag acatggaGCTGAGCagcctgag 1-02 acatggagctgagcaggctgag ................g..... 1-18 acatggagctgaggagcctgag .............g........ 5-51 acctgcagtggagcagcctgaa ..c..c..tg...........a 3-15 atctgcaaatgaacagcctgaa .tc..c.aa...a........a 3-30.3 atctgcaaatgaacagcctgag .tc..c.aa...a......... 3-20 atctgcaaatgaacagtctgag .tc..c.aa...a...t..... 7-4.1 atctgcagatctgcagcctaaa .tc..c..a.ct.......a.a 3-66 atcttcaaatgaacagcctgag .tc.tc.aa...a......... 3-64 atcttcaaatgggcagcctgag .tc.tc.aa..g.......... 4-30.1 ccctgaagctgagctctgtgac c.c..a........tctg...c 6-1 ccctgcagctgaactctgtgac c.c..c......a.tctg...c 2-70 tccttacaatgaccaacatgga t.c.tacaa...c..a.a..ga 2-26 tccttaccatgaccaacatgga t.c.tacca...c..a.a..ga Seqs with the expected RE site only....... 597 (counting sequences with 4 or fewer mismatches) Seqs with only an unexpected site......... 2 Seqs with both expected and unexpected.... 2 Seqs with no sites........................ 686 C: HpyCH4III, Bst4CI, or TaaI in HC In scoring whether the RE site of interest is present, only ONs that have 4 or fewer mismatches are counted. Number of sequences.......... 1617 Id Ntot 0 1 2 3 4 5 6 7 8 Ncut acngt acngt  1 244  79  92  43  18  10   1   2   0   0 241 102#1,1 ccgtgtattACTGTgcgagaga ccgtgtattactgtgcgagaga  2 457  69 150 115  66  34  11   8   3   1 434 103#2,3 ctqtgtattaatgtgcgaqaga .t....................  3 173  52  45  36  22  14   3   0   0   1 169 108#3 ccgtgtattactgtgcgagagg .....................g  4  16   0   3   2   2   1   6   0   1   1   8 124#5,1 ccgtgtattactgtgcaacaga ................a.c...  5   4   0   0   1   0   1   1   0   1   0   2 145#6 ccatgtattactgtgcaagata ..a.............a...t.  6  15   1   0   1   0   6   4   1   1   1   8 158#8 ccgtgtattactgtgcggcaga .................gc...  7  23   4   8   5   2   2   1   1   0   0  21 205#12 ccacatattactgtgcacacag ..aca...........acacag  8   9   1   1   1   0   3   2   1   0   0   6 226#13 ccacatattactgtgcacggat ..aca...........ac.gat  9   7   1   3   1   1   0   0   1   0   0   6 270#14 ccacgtattactgtgcacggat ..ac............ac.gat 10  23   7   3   5   5   2   1   0   0   0  22 309#16, ccttgtattactgtgcaaaaga ..t.............a.a... 11  35   5  10   7   6   3   3   0   1   0  31 313#18, ctgtgtattactgtgcaagaga .t..............a..... 12  18   2   3   2   2   6   1   0   2   0  15 315#19 ccgtgtattactgtaccacaga ..............a.c.c... 13   3   1   2   0   0   0   0   0   0   0   3 320#20 ccttgtatcactgtgcgagaga ..tc.....c............ 14 117  29  23  28  22   8   4   2   1   0 110 323#22 ccgtatattactgtgcgaaaga ....a.............a... 15  75  21  25  13   9   1   4   2   0   0  69 330#23, ctgtgtattactgtgcgaaaga .t................a... 16  14   2   2   2   3   0   3   1   1   0   9 349#29 ccgtgtattactgtactagaga ..............a.t..... 17   2   0   0   1   0   0   1   0   0   0   1 372#33 ccgtgtattactgtgctagaga ................t..... 18   1   0   0   1   0   0   0   0   0   0   1 373#34 ccgtgtattactgtactagaca ..............a.t...c. 19   2   0   0   0   0   0   0   0   0   2   0 3d#36 ctgtgtattactgtaagaaaga .t............aa..a... 20  34   4   9   9   4   5   3   0   0   0  31 428#38 ccgtgtattactgtgcgagaaa ....................a. 21  17   5   4   2   2   3   1   0   0   0  16 4302#40 ccgtgtattactgtgccagaga ................c..... 22  75  15  17  24   7  10   1   1   0   0  73 439#44 ctgtgtattactgtgcgagaca .t..................c. 23  40  14  15   4   5   1   0   1   0   0  39 551#48 ccatgtattactgtgcgagaca ..a.................c. 24 213  26  56  60  42  20   7   2   0   0 204 5a#49 ccatatattactgtgcgagaAA ..a.................AA Group 337 471  363  218  130   58   23   11    6 Cumulative 337 808 1171 1389 1519 1577 1600 1611 1617 Seqs with the expected RS site only.......1511 Seqs with only an unexpected site......... 0

[0164] Seqs with both expected and unexpected....8 Seqs with no sites........................0 Analysis repeated using only 8 best REdaptors Id Ntot 0 1 2 3 4 5 6 7 8+ 1 301 78 101 54 32 16 9 10 1 0 281 102#1 ccgtgtattactgtgcgagaga 2 493 69 155 125 73 37 14 11 3 6 459 103#2 ctgtgtattactgtgcgagaga 3 189 52 45 38 23 18 5 4 1 3 176 108#3 ccgtgtattactgtgcgagagg 4 127 29 23 28 24 10 6 5 2 0 114 323#22 ccgtatattactgtgcgaaaga 5 78 21 25 14 11 1 4 2 0 0 72 330#23 ctgtgtattactgtgcgaaaga 6 79 15 17 25 8 11 1 2 0 0 76 439#44 ctgtgtattactgtgcgagaca 7 43 14 15 5 5 3 0 1 0 0 42 551#48 ccatgtattactgtgcgagaca 8 307 26 63 72 51 38 24 14 13 6 250  5a#49 ccatgtattactgtgcgaga 1 102#1 ccgtgtattactgtgcgagaga ccgtgtattactgtgcgagaga 2 103#2 ctgtgtattactgtgcgagaga    .t.................... 3 108#3 ccgtgtattactgtgcgagagg    .....................g 4 323#22 ccgtatattactgtgcgaaaga    ....a.............a... 5 330#23 ctgtgtattactgtgcgaaaga    .t................a... 6 439#44 ctgtgtattactgtgcgagaca    .t.................c. 7 551#48 ccatgtattactgtgcgagaca    ..a.................c. 8  5a#49 ccatgtattactgtgcgagaAA ..a.................AA Segs with the expected RE site only........1463/1617 Segs with only an unexpected site..........   0 Segs with both expected and unexpected.....   7 Segs with no sites.........................   0

[0165] TABLE 300 Kappa FR1 GLGs ! 1   2   3   4   5   6   7   8   9   10  11  12   GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT ! 13  14  15  16  17  18  19  20  21  22  23   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  O12   GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  O2   GAC ATC CAG ATG ACC CAG TCT CCA TCC TCG CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  O18   GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  O8   GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  A20   GAC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  A30   AAC ATC CAG ATG ACC CAG TCT CCA TCT GCC ATG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !  L14   GAC ATC CAG ATG ACC CAG TCT CCA TCC TCA CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !  L1   GAC ATC CAG ATG ACC CAG TCT CCA TCC TCA CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !  L15   GCC ATC CAG TTG ACC CAG TCT CCA TCC TCC CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  L4   GCC ATC CAG TTG ACC CAG TCT CCA TCC TCC CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  L18   GAC ATC CAG ATG ACC CAG TCT CCA TCT TCC GTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !  L5   GAC ATC CAG ATG ACC CAG TCT CCA TCT TCT GTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGT  !  L19   GAC ATC CAG TTG ACC CAG TCT CCA TCC TTC CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  L8   GCC ATC CGG ATG ACC CAG TCT CCA TTC TCC CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  L23   GCC ATC CGG ATG ACC CAG TCT CCA TCC TCA TTC TCT   GCA TCT ACA GGA GAC AGA GTC ACC ATC ACT TGT  !  L9   GTC ATC TGG ATG ACC CAG TCT CCA TCC TTA CTC TCT   GCA TCT ACA GGA GAC AGA GTC ACC ATC AGT TGT  !  L24   GCC ATC CAG ATG ACC CAG TCT CCA TCC TCC CTG TCT   GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  L11   GAC ATC CAG ATG ACC GAG TCT CCT TCC ACC CTG TCT  !     GCA TCT GTA GGA GAC AGA GTC ACC ATC ACT TGC  !  L12   GAT ATT GTG ATG ACC CAG ACT CCA CTC TCC CTG CCC   GTC ACC CCT GGA GAG CCG GCC TCC ATC TCC TGC  !  O11   GAT ATT GTG ATG ACC CAG ACT CCA CTC TCC CTG CCC   GTC ACC CCT GGA GAG CCG GCC TCC ATC TCC TGC  !  O1   GAT GTT GTG ATG ACT CAG TCT CCA CTC TCC CTG CCC   GTC ACC CTT GGA CAG CCG GCC TCC ATC TCC TGC  !  A17   GAT GTT GTG ATG ACT CAG TCT CCA CTC TCC CTG CCC   GTC ACC CTT GGA CAG CCG GCC TCC ATC TCC TGC  !  A1   GAT ATT GTG ATG ACC CAG ACT CCA CTC TCT CTG TCC   GTC ACC CCT GGA CAG CCG GCC TCC ATC TCC TGC  !  A18   GAT ATT GTG ATG ACC CAG ACT CCA CTC TCT CTG TCC   GTC ACC CCT GGA GAG CCG GCC TCC ATC TCC TGC  !  A2   GAT ATT GTG ATG ACT CAG TCT CCA CTC TCC CTG CCC   GTC ACC CCT GGA GAG CCG GCC TCC ATC TCC TGC  !  A19   GAT ATT GTG ATG ACT CAG TCT CCA CTC TCC CTG CCC   GTC ACC CCT GGA GAG CCG GCC TCC ATC TCC TGC  !  A3   GAT ATT GTG ATG ACC CAG ACT CCA CTC TCC TCA CCT   GTC ACC CTT GGA GAG CCG GCC TCC ATC TCC TGC  !  A23   GAA ATT GTG TTG ACG CAG TCT CCA GGC ACC CTG TCT   TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !  A27   GAA ATT GTG TTG ACG CAG TCT CCA GCC ACC CTG TCT   TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !  A11   GAA ATA GTG ATG ACG CAG TCT CCA GCC ACC CTG TCT   GTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !  L2   GAA ATA GTG ATG ACG CAG TCT CCA GCC ACC CTG TCT   GTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !  L16   GAA ATT GTC TTG ACA CAG TCT CCA GCC ACC CTG TCT   TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !  L6   GAA ATT GTG TTG ACA CAG TCT CCA GCC ACC CTG TCT   TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TCG  !  L20   GAA ATT GTA ATG ACA CAG TCT CCA GCC ACC CTG TCT   TTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !  L25   GAC ATC GTG ATG ACC CAG TCT CCA GAC TCC CTG GCT   GTG TCT CTG GGC GAG AGG GCC ACC ATC AAC TGC  !  B3   GAA ACG ACA CTC ACG CAG TCT CCA GCA TTC ATG TCA   GCG ACT CCA GGA GAC AAA GTC AAC ATC TCC TGC  !  B2   GAA ATT GTG CTG ACT CAG TCT CCA GAC TTT GAG TCT   GTG ACT CCA AAG GAG AAA GTC ACC ATC ACC TGC  !  A26   GAA ATT GTG CTG ACT CAG TCT CCA GAC TTT CAG TCT   GTG ACT CCA AAG GAG AAA GTC ACC ATC ACC TGC  !  A10   GAT GTT GTG ATG ACA CAG TCT CCA GCT TTC CTC TCT   GTG ACT CCA GGG GAG AAA GTC ACC ACG ACC TGC  !  A14

[0166] TABLE 302 RERS sites found in Human Kappa FR1 GLGs FokI HPyCH MslI → ← → PflFI BsrI BsmAI MnlI 4V VKI O12    1-69    3    3   23   12   49   15   18   47   26   36 O2  101-169  103  103  123  112  149  115  118  147  126  136 O18  201-269  203  203  223  212  249  215  218  247  226  236 O8  301-369  303  303  323  312  349  315  318  347  326  336 A20  401-469  403  403  423  412  449  415  418  447  426  436 A30  501-569  503  503  523  512  549  515  518  547  526  536 L14  601-669  603  603  612  649  615  618  647 —  636 L1  701-769  703  703  723  712  749  715  718  747  726  736 L15  801-869  803  803  823  812  849  815  818  847  826  836 L4  901-969 —  903  923  912  949  906  915  918  947  926  936 L18 1001-1069 — 1003 1012 1049 1006 1015 1018 1047 1026 1036 L5 1101-1169 1103 — 1112 1149 1115 1118 1147 — 1136 L19 1201-1269 1203 1203 1212 1249 1215 1218 1247 — 1236 L8 1301-1369 — 1303 1323 1312 1349 1306 1315 1318 1347 — 1336 L23 1401-1469 1403 1403 1408 1412 1449 1415 1418 1447 — 1436 L9 1501-1569 1503 1503 1508 1523 1512 1549 1515 1518 1547 1526 1536 L24 1601-1669 1603 1608 1623 1612 1649 1615 1618 1647 — 1636 L11 1701-1769 1703 1703 1723 1712 1749 1715 1718 1747 1726 1736 L12 1801-1869 1803 1803 1812 1849 1815 1818 1847 — 1836 VKII O11 1901-1969 — — — — — 1956 — O1 2001-2069 — — — — 2056 — A17 2101-2169 — — 2112 — 2118 2156 — A1 2201-2269 — — 2212 — 2218 2256 — A18 2301-2369 — — — — — 2356 — A2 2401-2469 — — — — — 2456 — A19 2501-2569 — — 2512 — 2518 2556 — A3 2601-2669 — — 2612 — 2618 2656 — A23 2701-2769 — — — — — 2729 2756 — VKIII A27 2801-2869 — — 2812 — 2818 2839 — 2860 — A11 2901-2969 — — 2912 — 2918 2939 — 2960 — L2 3001-3069 — — 3012 — 3018 3039 — — 3060 L16 3101-3169 — — 3112 — 3118 3139 — 3160 L6 3201-3269 — — 3212 — 3218 3239 — 3260 L20 3301-3369 — — 3312 — 3318 3339 — 3360 L25 3401-3469 — — 3412 — 3418 3439 — 3460 VKIV B3 3501-3569 3503 — 3512 3515 3518 3539 — 3551< VKV B2 3601-3669 — — 3649 — 3618 3647 — VKVI A26 3701-3769 — — 3712 — 3718 — A10 3801-3869 — — 3812 — 3818 — A14 3901-3969 — — 3912 — 3918 3930> — MaeIII HpaII MlyI Tsp45I HphI MspI SfaNI SfcI HinfI →→ ← same sites xx38 xx56 xx62 xx06 xx52 VKI O12    1-69   37   41   53   53   55   56 — O2  101-169  137  141  153  153  155  156 — O18  201-269  237  241  253  253  255  256 — O8  301-369  337  341  353  353  355  356 — A20  401-469  437  441  453  453  455  456 — A30  501-569  537  541  553  553  555  556 — L14  601-669  637  641  653  653  655  656 — L1  701-769  737  741  753  753  755  756 — L15  801-869  837  841  853  853  855  856 — L4  901-969  937  941  953  953  955  956 — L18 1001-1069 1037 1041 1053 1053 1055 1056 — L5 1101-1169 1137 1141 1153 1153 1155 1156 — L19 1201-1269 1237 1241 1253 1253 1255 1256 — L8 1301-1369 1337 1341 1353 1353 1355 1356 — L23 1401-1469 1437 1441 1453 1453 1455 1456 1406 L9 1501-1569 1537 1541 1553 1553 1555 1556 1506 L24 1601-1669 1637 1641 1653 1653 1655 1656 L11 1701-1769 1737 1741 1753 1753 1755 1756 L12 1801-1869 1837 1841 1853 1853 1855 1856 VKII O11 1901-1969 — — 1918 1918 1937 1938 1952 O1 2001-2069 — — 2018 2018 2037 2038 2052 A17 2101-2169 — — 2112 2112 2137 2138 2152 A1 2201-2269 — — 2212 2212 2237 2238 2252 A18 2301-2369 — — 2318 2318 2337 2336 2352 A2 2401-2469 — — 2418 2418 2437 2436 2452 A19 2501-2569 — — 2512 2512 2537 2538 2552 A3 2601-2669 — — 2612 2612 2637 2638 2652 A23 2701-2769 — — 2718 2718 2737 2731* 2738* — VKIII A27 2801-2669 — — — — — A11 2901-2969 — — — — — L2 3001-3069 — — — — — L16 3101-3169 — — — — — L6 3201-3269 — — — — — L20 3301-3369 — — — — — L25 3401-3469 — — — — — VKIV B3 3501-3569 — — 3525 3525 — VKV B2 3601-3669 — — 3639 3639 — VKVI A26 3701-3769 — — 3712 3739 3712 3739 3737 3755 3756 3762 — A10 3801-3869 — — 3812 3839 3812 3839 3837 3855 3856 3862 — A14 3901-3969 — — 3939 3939 3937 3955 3956 3962 — BsrFI Cac8I BpmI NaeI BsaJI BssKI (NstNI) xx20 xx41 xx44 NgoMI HaeII xx29 xx42 xx43 xx22 xx30 xx43 →→ ← V I Tsp509I VKI O12    1-69 — — — — — — O2  101-169 — — — — — — O18  201-269 — — — — — — O8  301-369 — — — — — — A20  401-469 — — — — — — A30  501-569 — — — — — — L14  601-669 — — — — — — L1  701-769 — — — — — — L15  801-869 — — — — — — L4  901-969 — — — — — — L18 1001-1069 — — — — — — L5 1101-1169 — — — — — — L19 1201-1269 — — — — — — L8 1301-1369 — — — — — — L23 1401-1469 — — — — — — L9 1501-1569 — — — — — — L24 1601-1669 — — — — — — L11 1701-1769 — — — — — — L12 1801-1869 — — — — — — VKII O11 1901-1969 1942 1943 1944 1951 1954 — O1 2001-2069 2042 2043 2044 2051 2054 — A17 2101-2169 2142 — — 2151 2154 — A1 2201-2269 2242 — — 2251 2254 — A18 2301-2369 2342 2343 — 2351 2354 — A2 2401-2469 2442 2443 — 2451 2454 — A19 2501-2569 2542 2543 2544 2551 2554 — A3 2601-2669 2642 2643 2644 2651 2654 — A23 2701-2769 2742 — — 2751 2754 — VKIII A27 2801-2869 2843 2822 2843 2820 2841 — — 2803 A11 2901-2969 2943 2943 2920 2941 — — 2903 L2 3001-3069 3043 3043 3041 — — — L16 3101-3169 3143 3143 3120 3141 — — — L6 3201-3269 3243 3243 3220 3241 — — 3203 L20 3301-3369 3343 3343 3320 3341 — — — 3303 L25 3401-3469 3443 3443 3420 3441 — — 3403 VKIV B3 3501-3569 3529 3530 3520 — 3554 VKV B2 3601-3669 3643 3620 3641 — — VKVI A26 3701-3769 — 3720 — — 3703 A10 3801-3869 — 3820 — — 3803 A14 3901-3969 3943 3943 3920 3941 — — —

[0167] TABLE 400 Lambda FR1 GLG sequences ! VL1 CAG TCT GTG CTG ACT CAG CCA CCC TCG GTG TCT GAA GCC CCC AGG CAG AGG GTC ACC ATC TCC TGT !  1a cag tct gtg gtg acG cag ccG ccc tcA gtg tct gGG gcc ccA Ggg cag agg gtc acc atc tcc tgC !  1e cag tct gtg ctg act cag cca ccc tcA gCg tct gGG Acc ccc Ggg cag agg gtc acc atc tcT tgt !  1c cag tct gtg ctg act cag cca ccc tcA gCg tct gGG Acc ccc Ggg cag agg gtc acc atc tcT tgt !  1g cag tct gtg Ttg acG cag ccG ccc tcA gtg tct gCG gcc ccA GgA cag aAg gtc acc atc tcc tgC !  1b ! VL2 CAG TCT GCC CTG ACT CAG CCT CCC TCC GCG TCC GGG TCT CCT GGA CAG TCA GTC ACC ATC TCC TGC !  2c cag tct gcc ctg act cag cct cGc tcA gTg tcc ggg tct cct gga cag tca gtc acc atc tcc tgc !  2e cag tct gcc ctg act cag cct Gcc tcc gTg tcT ggg tct cct gga cag tcG Atc acc atc tcc tgc !  2a2 cag tct gcc ctg act cag cct ccc tcc gTg tcc ggg tct cct gga cag tca gtc acc atc tcc tgc !  2d cag tct gcc ctg act cag cct Gcc tcc gTg tcT ggg tct cct gga cag tcG Atc acc atc tcc tgc !  2b2 ! VL3 TCC TAT GAG CTG ACT CAG CCA CCC TCA GTG TCC GTG TCC CCA GGA CAG ACA GCC AGC ATC ACC TGC !   3r tcc tat gag ctg act cag cca cTc tca gtg tcA gtg Gcc cTG gga cag acG gcc agG atT acc tgT !  3j tcc tat gag ctg acA cag cca ccc tcG gtg tcA gtg tcc cca gga caA acG gcc agG atc acc tgc !  3p tcc tat gag ctg acA cag cca ccc tcG gtg tcA gtg tcc cTa gga cag aTG gcc agG atc acc tgc !  3a tcT tCt gag ctg act cag GAC ccT GcT gtg tcT gtg Gcc TTG gga cag aca gTc agG atc acA tgc !  3l tcc tat gTg ctg act cag cca ccc tca gtg tcA gtg Gcc cca gga Aag acG gcc agG atT acc tgT !  3h tcc tat gag ctg acA cag cTa ccc tcG gtg tcA gtg tcc cca gga cag aca gcc agG atc acc tgc !  3e tcc tat gag ctg aTG cag cca ccc tcG gtg tcA gtg tcc cca gga cag acG gcc agG atc acc tgc !  3m tcc tat gag ctg acA cag cca Tcc tca gtg tcA gtg tcT ccG gga cag aca gcc agG atc acc tgc !  V2-19 ! VL4 CTG CCT GTG CTG ACT CAG CCC CCG TCT GCA TCT GCC TTG CTG GGA GCC TCG ATC AAG CTC ACC TGC !  4c cAg cct gtg ctg act caA TcA TcC tct gcC tct gcT tCC ctg gga Tcc tcg Gtc aag ctc acc tgc !  4a cAg cTt gtg ctg act caA TcG ccC tct gcC tct gcc tCC ctg gga gcc tcg Gtc aag ctc acc tgc !  4b ! VL5 CAG CCT GTG CTG ACT CAG CCA CCT TCC TCC TCC GCA TCT CCT GGA GAA TCC GCC AGA CTC ACC TGC !  5e cag Gct gtg ctg act cag ccG Gct tcc CTc tcT gca tct cct gga gCa tcA gcc agT ctc acc tgc !  5c cag cct gtg ctg act cag cca Tct tcc CAT tcT gca tct Tct gga gCa tcA gTc aga ctc acc tgc !  5b ! VL6 AAT TTT ATG CTG ACT CAG CCC CAC TCT GTG TCG GAG TCT CCG GGG AAG ACG GTA ACC ATC TCC TGC !  6a ! VL7 CAG ACT GTG GTG ACT CAG GAG CCC TCA CTG ACT GTG TCC CCA GGA GGG ACA GTC ACT CTC ACC TGT !  7a cag Gct gtg gtg act cag gag ccc tca ctg act gtg tcc cca gga ggg aca gtc act ctc acc tgt !  7b ! VL8 CAG ACT GTG GTG ACC CAG GAG CCA TCG TTG TCA GTG TCC CCT GGA GGG ACA GTC ACA CTC ACT TGT !  8a ! VL9 CAG CCT GTG CTG ACT CAG CCA CCT TCT GCA TCA GCC TCC CTG GGA GCC TCG GTC ACA CTC ACC TGC !  9a ! VL10 CAG GCA GGG CTG ACT CAG CCA CCC TCG GTG TCC AAG GGC TTG AGA CAG ACC GCC ACA CTC ACC TGC !  10a

[0168] TABLE 405 RERSs found in human lambda FR1 GLGs ! There are 31 lambda GLGs MlyI NnnnnnGACTC   25  1: 6  3: 6  4: 6  6: 6  7: 6  8: 6  9: 6 10: 6 11: 6 12: 6 15: 6 16: 6 20: 6 21: 6 22: 6 23: 6 23: 50 24: 6 25: 6 25: 50 26: 6 27: 6 28: 6 30: 6 31: 6 There are 23 hits at base# 6 -“- GAGTCNNNNNn 1 26: 34 MwoI GCNNNNNnngc   20  1: 9  2: 9  3: 9  4: 9 11: 9 11: 56 12: 9 13: 9 14: 9 16: 9 17: 9 18: 9 19: 9 20: 9 23: 9 24: 9 25: 9 26: 9 30: 9 31: 9 There are 19 hits at base# 9 HinfI Gantc          27  1: 12  3: 12  4: 12  6: 12  7: 12  8: 12  9: 12 10: 12 11: 12 12: 12 15: 12 16: 12 20: 12 21: 12 22: 12 23: 12 23: 46 23: 56 24: 12 25: 12 25: 56 26: 12 26: 34 27: 12 28: 12 30: 12 31: 12 There are 23 hits at base# 12 PleI gactc          25  1: 12  3: 12  4: 12 6: 12  7: 12  8: 12  9: 12 10: 12 11: 12 12: 12 15: 12 16: 12 20: 12 21: 12 22: 12 23: 12 23: 56 24: 12 25: 12 25: 56 26: 12 27: 12 28: 12 30: 12 31: 12 There are 23 hits at base# 12 -“- gagtc          1 26: 34 DdeI Ctnag          32  1: 14  2: 24  3: 14  3: 24  4: 14  4: 24  5: 24  6: 14  7: 14  7: 24  8: 14  9: 14 10: 14 11: 14 11: 24 12: 14 12: 24 15: 5 15: 14 16: 14 16: 24 19: 24 20: 14 23: 14 24: 14 25: 14 26: 14 27: 14 28: 14 29: 30 30: 14 31: 14 There are 21 hits at base# 14 BsaJI Ccnngg          38  1: 23  1: 40  2: 39  2: 40  3: 39  3: 40  4: 39  4: 40  5: 39 11: 39 12: 38 12: 39 13: 23 13: 39 14: 23 14: 39 15: 38 16: 39 17: 23 17: 39 18: 23 18: 39 21: 38 21: 39 21: 47 22: 38 22: 39 22: 47 26: 40 27: 39 28: 39 29: 14 29: 39 30: 38 30: 39 30: 47 31: 23 31: 32 There are 17 hits at base# 39 There are 5 hits at base# 38 There are 5 hits at base# 40 Makes cleavage ragged. MnlI cctc          35  1: 23  2: 23  3: 23  4: 23  5: 23  6: 19  6: 23  7: 19  8: 23  9: 19  9: 23 10: 23 11: 23 13: 23 14: 23 16: 23 17: 23 18: 23 19: 23 20: 47 21: 23 21: 29 21: 47 22: 23 22: 29 22: 35 22: 47 23: 26 23: 29 24: 27 27: 23 28: 23 30: 35 30: 47 31: 23 There are 21 hits at base# 23 There are 3 hits at base# 19 There are 3 hits at base# 29 There are 1 hits at base# 26 There are 1 hits at base# 27 These could make cleavage ragged. -“- gagg          7  1: 48  2: 48  3: 48  4: 48 27: 44 28: 44 29: 44 BssKI Nccngg          39  1: 40  2: 39  3: 39  3: 40  4: 39  4: 40  5: 39  6: 31  6: 39  7: 31  7: 39  8: 39  9: 31  9: 39 10: 39 11: 39 12: 38 12: 52 13: 39 13: 52 14: 52 16: 39 16: 52 17: 39 17: 52 18: 39 18: 52 19: 39 19: 52 21: 38 22: 38 23: 39 24: 39 26: 39 27: 39 28: 39 29: 14 29: 39 30: 38 There are 21 hits at base# 39 There are 4 hits at base# 38 There are 3 hits at base# 31 There are 3 hits at base# 40 Ragged BstNI CCwgg          30  1: 41  2: 40  5: 40  6: 40  7: 40  8: 40  9: 40 10: 40 11: 40 12: 39 12: 53 13: 40 13: 53 14: 53 16: 40 16: 53 17: 40 17: 53 18: 40 18: 53 19: 53 21: 39 22: 39 23: 40 24: 40 27: 40 28: 40 29: 15 29: 40 30: 39 There are 17 hits at base# 40 There are 7 hits at base# 53 There are 4 hits at base# 39 There are 1 hits at base# 41 Ragged PspGI ccwgg          30  1: 41  2: 40  5: 40  6: 40  7: 40  8: 40  9: 40 10: 40 11: 40 12: 39 12: 53 13: 40 13: 53 14: 53 16: 40 16: 53 17: 40 17: 53 18: 40 18: 53 19: 53 21: 39 22: 39 23: 40 24: 40 27: 40 28: 40 29: 15 29: 40 30: 39 There are 17 hits at base# 40 There are 7 hits at base# 53 There are 4 hits at base# 39 There are 1 hits at base# 41 ScrFI CCngg          39  1: 41  2: 40  3: 40  3: 41  4: 40  4: 41  5: 40  6: 32  6: 40  7: 32  7: 40  8: 40  9: 32  9: 40 10: 40 11: 40 12: 39 12: 53 13: 40 13: 53 14: 53 16: 40 16: 53 17: 40 17: 53 18: 40 18: 53 19: 40 19: 53 21: 39 22: 39 23: 40 24: 40 26: 40 27: 40 28: 40 29: 15 29: 40 30: 39 There are 21 hits at base# 40 There are 4 hits at base# 39 There are 3 hits at base# 41 MaeIII gtnac          16  1: 52  2: 52  3: 52  4: 52  5: 52  6: 52  7: 52  9: 52 26: 52 27: 10 27: 52 28: 10 28: 52 29: 10 29: 52 30: 52 There are 13 hits at base# 52 Tsp45I gtsac          15  1: 52  2: 52  3: 52  4: 52  5: 52  6: 52  7: 52  9: 52 27: 10 27: 52 28: 10 28: 52 29: 10 29: 52 30: 52 There are 12 hits at base# 52 HphI tcacc          26  1: 53  2: 53  3: 53 4: 53  5: 53  6: 53  7: 53  8: 53  9: 53 10: 53 11: 59 13: 59 14: 59 17: 59 18: 59 19: 59 20: 59 21: 59 22: 59 23: 59 24: 59 25: 59 27: 59 28: 59 30: 59 31: 59 There are 16 hits at base# 59 There are 10 hits at base# 53 BspMI ACCTGCNNNNn          14 11: 61 13: 61 14: 61 17: 61 18: 61 19: 61 20: 61 21: 61 22: 61 23: 61 24: 61 25: 61 30: 61 31: 61 There are 14 hits at base# 61 Goes into CDR1

[0169] TABLE 500 h3401-h2 captured Via CJ with BsmAI !  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 !  S   A   Q   D   I   Q   M   T   Q   S   P   A   T   L   S   a GT GCA Caa gac atc cag atg acc cag tct cca gcc acc ctg tct !  ApaLI...                                 a gcc acc ! L25,L6,L20,L2,L16,A11 !  Extender.................................Bridge... ! 16  17  18  19  20  21  22  23  24  25  26  27  28  29  30 !  V   S   P   G   E   R   A   T   L   S   C   R   A   S   Q   gtg tct cca ggg gaa agg gcc acc ctc tcc tgc agg gcc agt cag ! 31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !  S   V   S   N   N   L   A   W   Y   Q   Q   K   P   G   Q agt gtt agt aac aac tta gcc tgg tac cag cag aaa cct ggc cag ! 46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !  V   P   R   L   L   I   Y   G   A   S   T   R   A   T   D   gtt ccc agg ctc ctc atc tat ggt gca tcc acc agg gcc act gat ! 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !  I   P   A   R   F   S   G   S   G   S   G   T   D   F   T   atc cca gcc agg ttc agt ggc agt ggg tct ggg aca gac ttc act ! 76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !  L   T   I   S   R   L   E   P   E   D   F   A   V   Y   Y   ctc acc atc agc aga ctg gag cct gaa gat ttt gca gtg tat tac ! 91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !  C   Q   R   Y   G   S   S   P   G   W   T   F   G   Q   G   tgt cag cgg tat ggt agc tca ccg ggg tgg acg ttc ggc caa ggg ! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !  T   K   V   E   I   K   R   T   V   A   A   P   S   V   F   acc aag gtg gaa atc aaa cga act gtg gct gca cca tct gtc ttc ! 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !  I   F   P   P   S   D   E   Q   L   K   S   G   T   A   S   atc ttc ccg cca tct gat gag cag ttg aaa tct gga act gcc tct ! 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 !  V   V   C   L   L   N   N   F   Y   P   R   E   A   K   V   gtt gtg tgc ctg ctg aat aac ttc tat ccc aga gag gcc aaa gta ! 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 !  Q   W   K   V   D   N   A   L   Q   S   G   N   S   Q   E   cag tgg aag gtg gat aac gcc ctc caa tcg ggt aac tcc cag gag ! 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !  S   V   T   E   Q   D   S   K   D   S   T   Y   S   L   S   agt gtc aca gag cag gac agc aag gac agc acc tac agc ctc agc ! 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 !  S   T   L   T   L   S   K   A   D   Y   E   K   H   K   V   agc acc ctg acg ctg agc aaa gca gac tac gag aaa cac aaa gtc ! 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !  Y   A   C   E   V   T   H   Q   G   L   S   S   P   V   T   tac gcc tgc gaa gtc acc cat cag ggc ctg agc tcg cct gtc aca ! 211 212 213 214 215 216 217 218 219 220 221 222 223 !  K   S   F   N   K   G   E   C   K   G   E   F   A   aag agc ttc aac aaa gga gag tgt aag ggc gaa ttc gc.....

[0170] TABLE 501 h3401-d8 KAPPA captured with CJ and BsmAI !  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 !  S   A   Q   D   I   Q   M   T   Q   S   P   A   T   L   S   a GT GCA C aa gac atc cag atg acc cag tct cct gcc acc ctg tct !  ApaLI...Extender......................... a  gcc acc ! L25,L6,L20,L2,L16,A11 !                                           A GCC ACC CTG TCT !L2 !  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30 !  V   S   P   G   E   R   A   T   L   S   C   R   A   S   Q   gtg tct cca ggt gaa aga gcc acc ctc tcc tgc agg gcc agt cag ! GTG TCT CCA GGG GAA AGA GCC ACC CTC TCC TGC  !     L2 !  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !  N   L   L   S   N   L   A   W   Y   Q   Q   K   P   G   Q   aat ctt ctc agc aac tta gcc tgg tac cag cag aaa cct ggc cag !  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 !  A   P   R   L   L   I   Y   G   A   S   T   G   A   I   G   gct ccc agg ctc ctc atc tat ggt gct tcc acc ggg gcc att ggt !  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 !  I   P   A   R   F   S   G   S   G   S   G   T   E   F   T   atc cca gcc agg ttc agt ggc agt ggg tct ggg aca gag ttc act !  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !  L   T   I   S   S   L   Q   S   E   D   F   A   V   Y   F   ctc acc atc agc agc ctg cag tct gaa gat ttt gca gtg tat ttc !  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !  C   Q   Q   Y   G   T   S   P   P   T   F   G   G   G   T   tgt cag cag tat ggt acc tca ccg ccc act ttc ggc gga ggg acc ! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !  K   V   E   I   K   R   T   V   A   A   P   S   V   F   I   aag gtg gag atc aaa cga act gtg gct gca cca tct gtc ttc atc ! 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !  F   P   P   S   D   E   Q   L   K   S   G   T   A   S   V   ttc ccg cca tct gat gag cag ttg aaa tct gga act gcc tct gtt ! 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 !  V   C   P   L   N   N   F   Y   P   R   E   A   K   V   Q   gtg tgc ccg ctg aat aac ttc tat ccc aga gag gcc aaa gta cag ! 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 !  W   K   V   D   N   A   L   Q   S   G   N   S   Q   E   S   tgg aag gtg gat aac gcc ctc caa tcg ggt aac tcc cag gag agt ! 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !  V   T   E   Q   D   N   K   D   S   T   Y   S   L   S   S   gtc aca gag cag gac aac aag gac agc acc tac agc ctc agc agc ! 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 !  T   L   T   L   S   K   V   D   Y   E   K   H   E   V   Y   acc ctg acg ctg agc aaa gta gac tac gag aaa cac gaa gtc tac ! 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !  A   C   E   V   T   H   Q   G   L   S   S   P   V   T   K   gcc tgc gaa gtc acc cat cag ggc ctt agc tcg ccc gtc acg aag ! 211 212 213 214 215 216 217 218 219 220 221 222 223 !  S   F   N   R   G   E   C   K   K   E   F   V   agc ttc aac agg gga gag tgt aag aaa gaa ttc gtt t

[0171] TABLE 508 Human heavy chains bases 88.1 to 94.2 Number of sequences..........   840 Number of Mismatchers......... Probe Id Ntot 0 1 2 3 4 5 6 7 Name Sequence............ Dot form............ 1 364 152 97 76 26 7 4 2 0 VHS881-1.1 gctgtgtattactgtgcgag gctgtgtattactgtgcgag 2 265 150 60 33 13 5 4 0 0 VHS881-1.2 gccgtgtattactgtgcgag ..c................. 3 96 14 34 16 10 5 7 9 1 VHS881-2.1 gccgtatattactgtgcgag ..c..a.............. 4 20 0 3 4 9 2 2 0 0 VHS881-4.1 gccgtgtattactgtacgag ..c............a.... 5 95 25 36 18 11 2 2 0 1 VHS881-9.1 gccatgtattactgtgcgag ..ca................ 840 341 230 147 69 21 19 11 2 341 571 718 787 808 827 838 840 88 89 90 91 92 93 94 95 Codon number as in Table 195 Recognition........... Stem...... Loop. Stem...... (VHS881-1.1) 5′-gctgtgtat|tact-gtgcgag cAcATccgTg TTgTT cAcggATgTg-3′ (VHS881-1.2) 5′-gccgtgtat|tact-gtgcgag cAcATccgTg TTgTT cAcggATgTg-3′ (VHS881-2.1) 5′-gccgtatat|tact-gtgcgag cAcATccgTg TTgTT cAcggATgTg-3′ (VHS881-4.1) 5′-gccgtgtat|tact-gtacgag cAcATccgTg TTgTT cAcggATgTg-3′ (VHS881-9.1) 5′-gccatgtat|tact-gtgccgag cAcATccgTg TTgTT cAcggATgTg-3′                  | site of substrate cleavage (FOKIact) 5′-cAcATccgTg TTgTT cAcggATgTg-3′ (VHEx881) 5′-AATAgTAgAc TgcAgTgTcc TcAgcccTTA AgcTgTTcAT cTgcAAgTAg- AgAgTATTcT TAgAgTTgTc TcTAgAcTTA gTgAAgcg-3′ ! note that VHEx881 is the reverse complement of the ON below ! [RC] 5′-cgCttcacTaag- ! Scab........ ! Synthetic 3-23 as in Table 206 ! |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- ! XbaI... ! |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|t-3′ ! AflII... (VHBA881) 5′-cgCttcacTaag- |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgt gcg ag-3′ (VHBB881) 5′-cgCttcacTaag- TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- |aac|agC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgt Acg ag-3′ (VH881PCR) 5′-cgCttcacTaag|TCT|AGA|gac|aac-3′

[0172] TABLE 512 Kappa, bases 12-30 ! ID Ntot 0 1 2 3 4 5 6 Name Sequence.......... Dot Form........... ! 1 84 40 21 20 1 2 0 0 SK12O12 gacccagtctccatcctcc gacccagtctccatcctcc ! 2 32 19 3 6 2 1 0 1 SK12A17 gactcagtctccactctcc ..t..........ct.... ! 3 26 17 8 1 0 0 0 0 SK12A27 gacgcagtctccaggcacc ..g..........gg.a.. ! 4 40 21 18 1 0 0 0 0 SK12A11 gacgcagtctccagccacc ..g..........g..a.. ! 182 97 50 28 3 3 0 1 ! 97 147 175 178 181 181 182 URE adapters: ! Stem...... Loop. Stem...... Recognition........ (SzKB1230-012) 5′-cAcATccgTg TTgTT cAcggATgTg ggAggATggAgAcTgggTc-3′ ! [RC] 5′-gacccagtctccatcctcc cAcATccgTg AAcAA cAcggATgTg-3′ ! Recognition........ Stem...... loop. Stem...... !                       FokI.            FokI. ! ! Stem...... Loop. Stem...... Recognition........ (SzKB1230-A17) 5′-cAcATccgTg TTgTT cAcggATgTg ggAgAgTggAgAcTgAgTc-3′ ! [RC] 5′-gactcagtctccactctcc cAcATccgTg AAcAA cAcggATgTg-3′ ! Recognition........ Stem...... loop. Stem...... !                       FokI.            FokI. ! ! Stem...... Loop. Stem...... Recognition........ (SzKB1230-A27) 5′-cAcATccgTg TTgTT cAcggATgTg ggTgccTggAgAcTgcgTc-3′ ! [RC] 5′-gacgcagtctccaggcacc cAcATccgTg AAcAA cAcggATgTg-3′ ! Recognition........ Stem...... loop. Stem...... !                       FokI.            FokI. ! ! Stem...... Loop. Stem...... Recognition........ (SzKB1230-All) 5′-cAcATccgTg TTgTT cAcggATgTg ggTggcTggAgAcTgcgTc-3′ ! [RC[ 5′-gacgcagtctccagccacc cAcATccgTg AAcAA cAcggATgTg-3′ ! Recognition........ Stem...... loop. Stem...... !                       FokI.            FokI. What happens in the upper strand: (SzKB1230-012*) 5′-gac cca gtc|tcc a-tc ctc c-3′ !                  | Site of cleavage in substrate ! (SzKB1230-A17*) 5′-gac tca gtc|tcc a-ct ctc c-3′ ! (SzKB1230-A27*) 5′-gac gca gtc|tcc a-gg cac c-3′ ! (SzKB1230-A11*) 5′-gac gca gtc|tcc a-gc cac c-3′ ! (kapextURE) 5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg-3′ !sense strand Scab.............ApaLI. (kapextUREPCR) 5′-ccTctactctTgTcAcAgTg-3′ Scab............. (kaBRO1UR) 5′-ggAggATggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ ! [RC]5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-tc ctc c-3′ ON above is R C. of this one (kaBRO2UR) 5′-ggAgAgTggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ ! [RC]5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-ct ctc c-3′ ON above is R.C. of this one (kaBRO3UR) 5′-ggTgccTggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ ! [RC]5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-gg cac c-3′ ON above is R.C. of this one (kaBRO4UR) 5′-ggTggcTggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ ! [RC]5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-gc cac c-3′ ON above is R.C. of this one Scab.............ApaLI. |TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|- |aac|aqC|TTA|AGg|gct|gag|gac|aCT|GCA|Gtc|tac|tat|tgt Acg ag-3′ (VH881PCR) 5′-cgCttcacTaag|TCT|AGA|gac|aac-3′

[0173] TABLE 512 Kappa, bases 12-30 ! ! ID Ntot 0 1 2 3 4 5 6 Name Sequence........... Dot Form........... ! 1 84 40 21 20 1 2 0 0 SK12012 gacccagtctccatcctcc gacccagtctccatcctcc ! 2 32 19 3 6 2 1 0 1 SK12A17 gactcagtctccactctcc ..t..........ct.... ! 3 26 17 8 1 0 0 0 0 SK12A27 gacgcagtctccaggcacc ...g.........gg.a.. ! 4 40 21 18 1 0 0 0 0 SK12A11 gacgcagtctccagccacc ...g.........g..a.. ! 182 97 50 28 3 3 0 1 ! 97 147 175 178 181 181 182 ! URE adapters: ! Stem...... Loop. Stem...... Recognition........ (SzKB1230-012) 5′-cAcATccgTg TTgTT cAcggATgTg ggAggATggAgAcTgggTc-3′ ! [RC] 5′-gacccagtctccatcctcc cAcATccgTg AAcAA cAcggATgTg-3′ ! Recognition........ Stem...... loop. Stem......                       FokI.            FokI. ! ! Stem...... Loop. Stem...... Recognition........ (SzKB1230-A17) 5′-cAcATccgTg TTgTT cAcggATgTg ggAgAgTggAgAcTgAgTc-3′ ! [RC] 5′-gactcagtctccactctcc cAcATccgTg AAcAA cAcggATqTg-3′ ! Recognition........ Stem...... loop. Stem......                       FokI.            FokI. ! Stem...... Loop. Stem...... Recognition........ (SzKB1230-A27) 5′-cAcATccgTg TTgTT cAcggATgTg ggTgccTggAgAcTgcgTc-3′ ! [RC] 5′-gacgcagtctccaggcacc cAcATccgTg AAcAA cAcggATgTg-3′ Recognition........ Stem...... loop. Stem......                       FokI.            FokI. Stem...... Loop. Stem...... Recognition........ (SzKB1230-A11) 5′-cAcATccgTg TTgTT cAcggATgTg ggTggcTggAgAcTgcgTc-3′ [RC] 5′-gacgcagtctccagccacc cAcATccgTg AAcAA cAcggATgTg-3′ Recognition........ Stem...... loop. Stem......                       FokI.            FokI. What happens in the upper strand: (SzKB1230-012*) 5′-gac cca gtc|tcc a-tc ctc c-3′ !               | Site of cleavage in substrate ! (SzKB1230-A17*) 5′-gac tca gtc|tcc a-ct ctc c-3′ ! (SzKB1230-A27*) 5′-gac gca gtc|tcc a-gg cac c-3′ ! (SzKB1230-A11*) 5′-gac gca gtc|tcc a-gc cac c-3′ (kapextURE) 5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg-3′ !sense strand Scab.............ApaLI. (kapextUREPGR) 5′-ccTctactctTgTcAcAgTg-3′ Scab............. (kaBRO1UR) 5′-ggAggATggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ ! [RC] 5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-tc ctc c-3′ ON above is R.C. of this one (kaBRO2UR) 5′-ggAgAgTggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ ! [RC] 5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-ct ctc c-3′ ON above is R.C. of this one (kaBRO3UR) 5′-ggTgccTggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ [RC] 5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-gg cac c-3′ ON above is R C. of this one (kaBRO4UR) 5′-ggTggcTggA cTggATgTcT TgTgcAcTgT gAcAAgAgTA gAgg-3′ ! [RC] 5′-ccTctactctTgTcAcAgTgcAcAA gAc ATc cAg tcc a-gc cac c-3′ ON above is R.C. of this one Scab.............ApaLI.

[0174] TABLE 515 Lambda URE adapters bases 13.3 to 19.3 ! ! Number of sequences.......... 128 ! ! Number of mismatches.............. ! Id Ntot 0 1 2 3 4 5 6 7 8 Name Sequence........... Dot form........... ! 1 58 45 7 1 0 0 0 2 2 1 VL133-2a2 gtctcctggacagtcgatc gtctcctggacagtcgatc ! 2 16 10 1 0 1 0 1 1 0 2 V1133-31 ggccttgggacagacagtc .g.cttg......a.ag.. ! 3 17 6 0 0 0 4 1 1 5 0 VL133-2c gtctcctggacagtcagtc ...............ag.. ! 4 37 3 0 10 4 4 3 7 4 2 VL133-1c ggccccagggcagagggtc .g.c..a..g...ag.g.. ! 128 64 8 11 5 8 5 11 11 5 ! 64 72 83 88 96 101 112 123 128 ! ! Stem...... loop. Stem...... Recognition........ (VL133-2a2) 5′-cAcATccgTg TTgTT cAcggATgTg gATcgAcTgTccAggAgAc-3′ ! [RC] 5′-gtctcctggacagtcgatc cAcATccgTg AAcAA cAcggATgTg-3′ Recognition........ Stem...... Loop. Stem...... ! ! Stem...... loop. Stem...... Recognition........ (VL133-31) 5′-cAcATccgTg TTgTT cAcggATgTg gAcTgTcTgTcccAAggcc-3′ ! [RC] 5′-ggccttgggacagacagtc cAcATccgTg AAcAA cAcggATgTg-3′ Recognition........ Stem...... Loop. Stem...... ! ! Stem...... loop. Stem...... Recognition........ (VL133-2c) 5′-cAcATccgTg TTgTT cAcggATgTg gAcTgAcTgTccAggAgAc-3′ [RC] 5′-gtctcctggacagtcagtc cAcATccgTg AAcAA cAcggATgTg-3′ ! Recognition........ Stem...... Loop. Stem...... ! ! Stem...... loop. Stem...... Recognition........ (VL133-1c) 5′-cAcATccgTg TTgTT cAcggATgTg gAcccTcTgcccTggggcc-3′ [RC] 5′-ggccccagggcagagggtc cAcATccgTg AAcAA cAcggATgTg-3′ What happens in the top strand: !               |site of cleavage in the upper strand (VL133-2a2*) 5′-g tct cct g|ga cag tcg atc ! (VL133-31*) 5′-g gcc ttg g|ga cag aca gtc ! (VL133-2c*) 5′-g tct cct g|ga cag tca gtc ! (VL133-1c*) 5′-g gcc cca g|gg cag agg gtc ! ! The following Extenders and Bridges all encode the AA sequence of 2a2 for codons 1-15 !                        1 (ON_LamEx133) 5′-ccTcTgAcTgAgT gcA cAg - ! !  2   3   4   5   6   7   8   9   10  11  12 AGt gcT TtA acC caA ccG gcT AGT gtT AGC ggT- ! !  13  14  15 tcC ccG g !  2a2 !                       1 (ON_LamB1-133) [RC] 5′-ccTcTgAcTgAgT gcA cAg - ! !  2   3   4   5   6   7   8   9   10  11  12 AGt gcT TtA acC caA ccG gcT AGT gtT AGC ggT- ! !  13  14  15 ! tcC ccG g ga cag tcg at-3′ ! 2a2 N.B. the actual seq is the                                 reverse complement of the                                 one shown. (ON_LamB2-133) [RC] 5′-ccTcTgAcTgAgT gcA cAg - !  2   3   4   5   6   7   8   9   10  11  12 AGt gcT TtA acC caA ccG gcT AGT gtT AGC ggT- !  13  14  15 tcC ccG g ga cag aca gt-3′ ! 31 N.B. the actual seq. is the !                                 reverse complement of the !                                 one shown. ! (ON_LamB3-133) [RC] 5′-ccTcTgAcTgAgT gcA cAg - !  2   3   4   5   6   7   8   9   10  11  12 AGt gcT TtA acC caA ccG gcT AGT gtT AGC ggT- !  13  14  15 tcC ccG g ga cag tca gt -3′! 2c N.B. the actual seq is the                                 reverse complement of the                                 one shown. (ON_LamB4-133) [RC] 5′-ccTcTgAcTgAgT gcA cAg - !  2   3   4   5   6   7   8   9   10  11  12 AGt gcT TtA acC caA ccG gcT AGT gtT AGC ggT- !  13  14  15 tcC ccG g gg cag agg gt-3′ ! 1c N.B. the actual seq is the                                 reverse complement of the                                 one shown. (ON_Lam133PCR) 5′-ccTcTgAcTgAgT gcA cAg AGt gc-3′

[0175] TABLE 525 ONs used in Capture of kappa light chains using CJ method and BsmAI All ONs are written 5′ to 3′. REdapters (6) ON_20SK15012 gggAggATggAgAcTgggTc ON_20SK15L12 gggAAgATggAgAcTgggTc ON_20SK15A17 gggAgAgTggAgAcTgAgTc ON_20SK15A27 gggTgccTggAgAcTgcgTc ON_20SK15A11 gggTggcTggAgAcTgcgTc ON_20SK15B3 gggAgTcTggAgAcTgggTc Bridges (6) kapbri1012 gggAggATggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg kapbri1L12 gggAAgATggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg kapbri1A17 gggAgAgTggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg kapbri1A27 gggTgccTggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg kapbri1A11 gggTggcTggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg kapbri1B3 gggAgTcTggAgAcTgggTcATcTggATgTcTTgTgcAcTgTgAcAgAgg Extender (5′biotinylated) kapext1bi ccTcTgTcAcAgTgcAcAAgAcATccAgATgAcccAgTcTcc Primers kaPCRt1 ccTcTgTcAcAgTgcAcAAgAc kapfor 5′-aca ctc tcc cct gtt gaa gct ctt-3′

[0176] TABLE 530 PCR program for amplification of kappa DNA 95° C. 5 minutes 95° C. 15 seconds 65° C. 30 seconds 72° C. 1 minute 72° C. 7 minutes  4° C. hold Reagents (100 ul reaction): Template 50 ng 10x turbo PCR buffer 1x turbo Pfu 4U dNTPs 200 μM each kaPCRt1 300 nM kapfor 300 nM

[0177] TABLE 610 Stuffer used in VH 1 TCCGGAGCTT CAGATCTGTT TGCCTTTTTG TGGGGTGGTG CAGATCGCGT TACGGAGATC 61 GACCGACTGC TTGAGCAAAA GCCACGCTTA ACTGCTGATC AGGCATGGGA TGTTATTCGC 121 CAAACCAGTC GTCAGGATCT TAACCTGAGG CTTTTTTTAC CTACTCTGCA AGCAGCGACA 181 TCTGGTTTGA CACAGAGCGA TCCGCGTCGT CAGTTGGTAG AAACATTAAC ACGTTGGGAT 241 GGCATCAATT TGCTTAATGA TGATGGTAAA ACCTGGCAGC AGCCAGGCTC TGCCATCCTG 301 AACGTTTGGC TGACCAGTAT GTTGAAGCGT ACCGTAGTGG CTGCCGTACC TATGCCATTT 361 GATAAGTGGT ACAGCGCCAG TGGCTACGAA ACAACCCAGG ACGGCCCAAC TGGTTCGCTG 421 AATATAAGTG TTGGAGCAAA AATTTTGTAT GAGGCGGTGC AGGGAGACAA ATCACCAATC 481 CCACAGGCGG TTGATCTGTT TGCTGGGAAA CCACAGCAGG AGGTTGTGTT GGCTGCGCTG 541 GAAGATACCT GGGAGACTCT TTCCAAACGC TATGGCAATA ATGTGAGTAA CTGGAAAACA 601 CCTGCAATGG CCTTAACGTT CCGGGCAAAT AATTTCTTTG GTGTACCGCA GGCCGCAGCG 661 GAAGAAACGC GTCATCAGGC GGAGTATCAA AACCGTGGAA CAGAAAACGA TATGATTGTT 721 TTCTCACCAA CGACAAGCGA TCGTCCTGTG CTTGCCTGGG ATGTGGTCGC ACCCGGTCAG 781 AGTGGGTTTA TTGCTCCCGA TGGAACAGTT GATAAGCACT ATGAAGATCA GCTGAAAATG 841 TACGAAAATT TTGGCCGTAA GTCGCTCTGG TTAACGAAGC AGGATGTGGA GGCGCATAAG 901 GAGTCGTCTA GA

[0178] TABLE 620 DNA sequence off pCEs5 ! pCES5 6680 bases=pCes4 with stuffers in CDR1-2 and CDR3 2000.12.13 ! ! Ngene=6680 ! Useful REs (cut MAnoLI fewer than 3 times) 2000.06.05 ! ! Non-cutters ! Acc65I Ggtacc AfeI AGCgct AvrII Cctagg ! BsaBI GATNNnnatc BsiWI Cqtacg BsmFI Nnnnnnnnnnnnnnngtccc ! BsrGI Tgtaca BstAPI GCANNNNntgc BstBI TTcgaa ! Bst817I GTAtac BtrI CACgtg Ecl136I GAGctc ! EcoRV GATatc FseI GGCCGGcc KpnI GGTACc ! MscI TGGcca NruI TCGcga NsiI ATGCAt ! PacI TTAATtaa PmeI GTTTaac PmlI CACgtg ! PpuMT RGgwccy PshAI GACNNnngtc SacI GAGCTc ! SacII CCGCgg SbfI CCTGCAgg SexAI Accwggt ! SgfI GCGATcgc SnaBI TACgta SpeI Actagt ! SphI GCATGc Sse8387I CCTGCAgg StuI AGGcct ! SwaI ATTTaaat XmaI Cccggg ! ! cutters ! Enzymes that cut more than 3 times. ! AlwNI CAGNNNctg 5 ! BsgI ctgcac 4 ! BsrFI Rccggy 5 ! EarI CTCTTCNnnn 4 ! FauI nNNNNNNGCGGG 10 ! ! Enzymes that cut from 1 to 3 times. ! ! Eco0109I RGgnccy 3 7 2636 4208 ! BssSI Ctcgtg 1 12 ! -″- Cacgag 1 1703 ! BspHI Tcatga 3 43 148 1156 ! AatII GACGTc 1 65 ! BciVI GTATCCNNNNNN 2 140 1667 ! Eco57I CTGAAG 1 301 ! -″- cttcag 2 1349 ! AvaI Cycgrg 3 319 2347 6137 ! BsiHKAI GWGCWc 3 401 2321 4245 ! HgiAI GWGCWc 3 401 2321 4245 ! BcgI gcannnnnntcg 1 461 ! ScaI AGTact 1 505 ! PvuI CGATcg 3 616 3598 5926 ! FspI TGCgca 2 763 5946 ! BglI GCCNNNNnggc 3 864 2771 5952 ! BpmI CTGGAG 1 898 ! -″- ctccag 1 4413 ! BsaI GGTCTCNnnnn 1 916 ! AhdI GACNNNnngtc 1 983 ! Eam1105I GACNNNnngtc 1 983 ! DrdI GACNNNNnngtc 3 1768 6197 6579 ! SapI gaagagc 1 1998 ! PvuII CAGctg 3 2054 3689 5896 ! PflMT CCANNNNntgg 3 2233 3943 3991 ! HindIII Aagctt 1 2235 ! ApaLI Gtgcac 1 2321 ! BspMI Nnnnnnnnngcaggt 1 2328 ! -″- ACCTGCNNNNn 2 3460 ! PstI CTGCAg 1 2335 ! AccI GTmkac 2 2341 2611 ! HincII GYYrac 2 2341 3730 ! SalI Gtcgac 1 2341 ! TliI Ctcgag 1 2347 ! XhoI Ctcgag 1 2347 ! BbsI gtcttc 2 2383 4219 ! BlpI GCtnagc 1 2580 ! EspI GCtnagc 1 2580 ! SgrAI CRccggyg 1 2648 ! AgeI Accggt 2 2649 4302 ! AscI GGcgcgcc 1 2689 ! BssHII Gcgcgc 1 2690 ! SfiI GGCCNNNNnggcc 1 2770 ! NaeI GCCggc 2 2776 6349 ! NgoMIV Gccggc 2 2776 6349 ! BtgI Ccrygg 3 2781 3553 5712 ! DsaI Ccrygg 3 2781 3553 5712 ! NcoI Ccatgg 1 2781 ! StyI Ccwwgg 3 2781 4205 4472 ! MfeI Caattg 1 2795 ! BspEI Tccgga 1 2861 ! BglII Agatct 1 2872 ! BclI Tgatca 1 2956 ! Bsu36I CCtnagg 3 3004 4143 4373 ! XcmI CCANNNNNnnnntgg 1 3215 ! MluI Acgcgt 1 3527 ! HpaI GTTaac 1 3730 ! XbaI Tctaga 1 3767 ! ! AflII Cttaag 1 3811 ! BsmI NGcattc 1 3821 ! -″- GAATGCN 1 4695 ! RsrII CGgwccg 1 3827 ! NheI Gctagc 1 4166 ! BstEII Ggtnacc 1 4182 ! BsmBI CGTCTCNnnnn 2 4188 6625 ! -″- Nnnnnngagacg 1 6673 ! ApaI GGGCCc 1 4209 ! BanII GRGCYc 3 4209 4492 6319 ! Bsp120I Gggccc 1 4209 ! PspOMI Gggccc 1 4209 ! BseRI NNnnnnnnnnctcctc 1 4226 ! -″- GAGGAGNNNNNNNNNN 1 4957 ! EcoNI CCTNNnnnagg 1 4278 ! PflFI GACNnngtc 1 4308 ! TthlllI GACNnngtc 1 4308 ! KasI Ggcgcc 2 4327 5967 ! BstXI CCANNNNNntgg 1 4415 ! NotI GCggccgc 1 4507 ! EagI Cggccg 1 4508 ! BamHI Ggatcc 1 5169 ! BspDI ATcgat 1 5476 ! NdeI CAtatg 1 5672 ! EcoRI Gaattc 1 5806 ! PsiI TTAtaa 1 6118 ! DraIII CACNNNgtg 1 6243 ! BsaAI YACgtr 1 6246 !---------------------------------------------------------------------------- 1 gacgaaaggg cCTCGTGata cgcctatttt tataggttaa tgtcatgata ataatggttt !             BssSI.(1 2) 61 cttaGACGTC aggtggcact tttcggggaa atgtgcgcgg aacccctatt tgtttatttt !     AatII. 121 tctaaataca ttcaaatatG TATCCgctca tgagacaata accctgataa atgcttcaat !                     BciVI..(1 of 2) 181 aatattgaaa aaggaagagt !Base # 201 to 1061=ApR gene from pUC119 with some RE sites removed ! !   1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 ! fM  S  I  Q  H  F  R  V  A  L  I  P  F  F  A 201 atg agt att caa cat ttc cgt gtc gcc ctt att ccc ttt ttt gcg ! !  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30 !  A  F  C  L  P  V  F  A  H  P  E  T  L  V  K 246 gca ttt tgc ctt cct gtt ttt gct cac cca gaa acg ctg gtg aaa ! !  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 ! V  K  D  A  E  D  Q  L  G  A  R  V  G  Y  I 291 gta aaa gat gct gaa gat cag ttg ggt gcc cga gtg ggt tac atc ! !  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 ! E  L  D  L  N  S  G  K  I  L  E  S  F  R  P 336 gaa ctg gat ctc aac agc ggt aag atc ctt gag agt ttt cgc ccc ! !  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75 ! E  E  R  F  P  M  M  S  T  F  K  V  L  L  C 381 gaa gaa cgt ttt cca atg atg agc act ttt aaa gtt ctg cta tgt ! !  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 ! G  A  V  L  S  R  I  D  A  G  Q  E  Q  L  G 426 ggc gcg gta tta tcc cgt att gac gcc ggg caa gaG CAa ctc ggT !                                               BcgI............ ! !  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 ! R  R  I  H  Y  S  Q  N  D   K   V   E   Y   S   P 471 CGc cgc ata cac tat tct cag aat gac ttg gtt gAG TAC Tca cca !..BcgI......                                              ScaI.... ! ! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !  V   T   E   K   H   L   T   D   G   M   T   V   R   E   L 516 gtc aca gaa aag cat ctt acg gat ggc atg aca gta aga gaa tta ! ! 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !  C   S   A   A   I   T   M   S   D   N   T   A   A   N   L 561 tgc agt gct gcc ata acc atg agt gat aac act gcg gcc aac tta ! ! 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 !  L   L   T   I   G   G   P   K   E   L   T   A   F   L 606 ctt ctg aca aCG ATC Gga gga ccg aag gag cta acc gct ttt ttg !              PvuI.... (1 2) ! ! 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 !  H   N   M   G   D   H   V   T   R   L   D   R   W   E   P 651 cac aac atg ggg gat cat gta act cgc ctt gat cgt tgg gaa ccg ! 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !  E   L   N   E   A   I   P   N   D   E   R   D   T   T   M 696 gag ctg aat gaa gcc ata cca aac gac gag cgt gac acc acg atg ! ! 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 !  P   V   A   M   A   T   T   L   R   K   L   L   T   G   E 741 cct gta GCA ATG gca aca acg tTG CGC Aaa cta tta act ggc gaa !         BsrDI..(1 2)         FspI.... (1 2) ! ! 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !  L   L   T   L   A   S   R   Q   Q   L   I   D   W   M   E 786 cta ctt act cta gct tcc cgg caa caa tta ata gac tgg atg gag ! ! 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 !  A   D   K   V   A   G   P   L   L   R   S   A   L   P   A 831 gcg gat aaa gtt gca gga cca ctt ctg cgc tcg gcc ctt ccg gct ! ! 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 !  G   W   F   I   A   D   K   S   G   A   G   E   R   G   S 876 ggc tgg ttt att gct gat aaa tCT GGA Gcc ggt gag cgt gGG TCT !                              BpmI....(1 2)           BsaI.... ! ! 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 !  R   G   I   I   A   A   L   G   P   D   G   K   P   S   R 921 Cgc ggt atC ATT GCa gca ctg ggg cca gat ggt aag ccc tcc cgt !BsaI......           BsrDI...(2 2) ! ! 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 !  I   V   V   I   Y   T   T   G   S   Q   A   T   M   D   E 966 atc gta gtt atc tac acG ACg ggg aGT Cag gca act atg gat gaa !                       AhdI........... ! ! 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 !  R   N   R   Q   I   A   E   I   G   A   S   L   I   K   H 1011 cga aat aga cag atc gct gag ata ggt gcc tca ctg att aag cat ! ! 286 287 !  W   . 1056 tgg taa 1062                                              ctgtcagac caagtttact 1081 catatatact ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga 1141 tcctttttga taatctcatg accaaaatcc cttaacgtga gttttcgttc cactgagcgt 1201 cagaccccgt agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct 1261 gctgcttgca aacaaaaaaa ccaccgctac cagcggtggt ttgtttgccg gatcaagagc 1321 taccaactct ttttccgaag gtaactggct tcagcagagc gcagatacca aatactgtcc 1381 ttctagtgta gccgtagtta ggccaccact tcaagaactc tgtagcaccg cctacatacc 1441 tcgctctgct aatcctgtta ccagtggctg ctgccagtgg cgataagtcg tgtcttaccg 1501 ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt 1561 cgtgcataca gcccagcttg gagcgaacga cctacaccga actgagatac ctacagcgtg 1621 agcattgaga aagcgccacg cttcccgaag ggagaaaggc ggacagGTAT CCggtaagcg !                                               BciVI.. (2 of 2) 1681 gcagggtcgg aacaggagag cgCACGAGgg agcttccagg gggaaacgcc tggtatcttt !                       BssSI.(2 2) 1741 atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag 1801 gggggcggag cctatggaaa aacgccagca acgcggcctt tttacggttc ctggcctttt 1861 gctggccttt tgctcACATG Ttctttcctg cgttatcccc tgattctgtg gataaccgta !                 PciI... 1921 ttaccgcctt tgagtgagct gataccgctc gccgcagccg aacgaccgag cgcagcgagt 1981 cagtgagcga ggaagcgGAA GAGGgcccaa tacgcaaacc gcctctcccc gcgcgttggc !                  SapI.... 2041 cgattcatta atgCAGCTGg cacgacaggt ttcccgactg gaaagcgggc agtgagcgca !              PvuII.(1 3) 2101 acgcaatTAA TGTgagttag ctcactcatt aggcacccca ggcTTTACAc tttatgcttc !        ..-35..        Plac                  ..-10. 2161 cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacaCAGGA AACAGCTATG !                                              M13Rev_seq_primer 2221 Accatgatta cgCCAAGCTT TGGagccttt tttttggaga ttttcaac !             PflMI....... 2221 ACcatgatta cgCCAAGCTT TGGagccttt tttttggaga ttttcaac !             PflMI....... !              Hind3. ! signal::linker::CLight ! !  1  2  3  4  5  6  7  8  9  10  11  12  13  14  15 ! fM   K   K   L   L   F   A   I   P   L   V   V   P   F   Y 2269 gtg aaa aaa tta tta ttc gca att cct tta gtt gtt cct ttc tat ! !               Linker.............................. End of FR4 !  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30 !  S   H   S   A   Q   V   Q   L   Q   V   D   L   E   I   K 2314 tct cac aGT GCA Cag gtc caa CTG CAG GTC GAC CTC GAG atc aaa !        ApaLI......          PstI...        XhoI... !                          BspMI... !                            SalI... !                            AccI...(1 2) !                            HincII.(1 2) ! ! Vlight domains could be cloned in as ApaLI-XhoI fragments. ! VL-CL (kappa) segments can be cloned in as ApaLI-AscI fragments. ! ! Ckappa---------------------------------------------------- !  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !  R   G   T   V   A   A   P   S   V   F   I   F   P   P   S 2359 cgt gga act gtg gct gca cca tct GTC TTC atc ttc ccg cca tct !                         BbsI...(1 2) ! !  46  47  48  49  50  51  52  53  54  55  56  57  58 59  60 !  D   E   Q   L   K   S   G   T   A   S   V   V   C   L   L 2404 gat gag cag ttg aaa tct gga act gcc tct gtt gtg tgc ctg ctg ! !  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  N   N   F   Y   P   R   E   A   K   V   Q   W   K   V   D 2449 aat aac ttc tat ccc aga gag gcc aaa gta cag tgg aag gtg gat ! !  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90 !  N   A   L   Q   S   G   N   S   Q   E   S   V   T   E   Q 2494 aac gcc ctc caa tcg ggt aac tcc cag gag agt gtc aca gag cag ! !  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 !  D   S   K   D   S   T   Y   S   L   S   S   T   L   T   L 2539 gac agc aag gac agc acc tac agc ctc agc agc acc ctg acG CTG !                                          EspI... ! ! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 !  S   K   A   D   Y   E   K   H   K   V   Y   A   C   E   V 2584 AGC aaa gca gac tac gag aaa cac aaa GTC TAC gcc tgc gaa gtc ! ...EspI....                            AccI...(2 2) ! 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 !  T   H   Q   G   L   S   S   P   V   T   K   S   F   N   R 2629 acc cat cag ggc ctg agt tcA CCG GTg aca aag agc ttc aac agg !                     AgeI....(1 2) ! ! 136 137 138 139 140 !  G   E   C   .   . 2674 gga gag tgt taa taa GG CGCGCCaatt !                AscI..... !                BssHII. 2701 ctatttcaag gagacagtca ta ! ! PelB::3-23(stuffed)::CHl::III fusion gene ! !   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15 !  M   K   Y   L   L   P   T   A   A   A   G   L   L   L   L 2723 atg aaa tac cta ttg cct acg gca gcc gct gga ttg tta tta ctc ! ! ---------------------------------------- ! !  16  17  18  19  20  21  22 !  A   A   Q   P   A   M   A 2768 gcG GCC cag ccG GCC atg gcc !   SfiI.............. !           NgcMIV..(1 2) !                  NcoI.... ! !                              FRl(DP47 V3-23)------------------- !                              23  23  24  25  26  27  28  29  30 !                               E   V   Q   L   L   E   S   G 2789                              gaa|gtt|CAA|TTG|tta|gag|tct|ggt| !                                     |MfeI| ! ! -------------FRl--------------------------------------------- !  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45 !   G   G   L   V   Q   P   G   G   S   L   R   L   S   C   A 2813 |ggc|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta|cgt|ctt|tct|tgc|gct| ! ! ----FRl----- !  46  47  48 !   A   S   G 2858 |gct|TCC|GGA| !     |BspEI| ! ! Stuffer for CDR1, FR2, and CDR2---------------------------------- ! There are no stp codons in this stuffer. 2867                                             gcttcAGATC Tgtttgcctt !                                                  BglII.. 2887 tttgtggggt ggtgcagatc gcgttacgga gatcgaccga ctgcttgagc aaaagccacg 2947 cttaactgcT GATCAggcat gggatgttat tcgccaaacc agtcgtcagg atcttaacct !          BclT... 3007 gaggcttttt ttacctactc tgcaagcagc gacatctggt ttgacacaga gcgatccgcg 3067 tcgtcagttg gtagaaacat taacacgttg ggatggcatc aatttgctta atgatgatgg 3127 taaaacctgg cagcagccag gctctgccat cctgaacgtt tggctgacca gtatgttgaa 3187 gcgtaccgta gtggctgccg tacctatgCC Atttgataag TGGtacagcg ccagtggcta !                             XcmI.............. 3247 cgaaacaacc caggacggcc caactggttc gctgaatata agtgttggag caaaaatttt 3307 gtatgaggcg gtgcagggag acaaatcacc aatcccacag gcggttgatc tgtttgctgg 3367 gaaaccacag caggaggttg tgttggctgc gctggaagat acctgggaga ctctttccaa 3427 acgctatggc aataatgtga gtaactggaa aacacctgca atggccttaa cgttccgggc 3487 aaataatttc tttggtgtac cgcaggccgc agcggaagaa ACGCGTcatc aggcggagta !                                         MluI.. 3547 tcaaaaccgt ggaacagaaa acgatatgat tgttttctca ccaacgacaa gcgatcgtcc 3607 tgtgcttgcc tgggatgtgg tcgcacccgg tcagagtggg tttattgctc ccgatggaac 3667 agttgataag cactatgaag atcagctgaa aatgtacgaa aattttggcc gtaagtcgct !                       PvuII. 3727 ctgGTTAACg aagcaggatg tggaggcgca taaggagtcg !    HpaI.. !    HincII(2 2) ! ! -------FR3------------------------------------------------ !          4   5   6   7   8   9  10  11  12  13  14  15  16 !          93  94  95  96  97  98 99 100 101 102 103 104 105 !          S   R   D   N   S   K   N  T   L   Y   L   Q   M 3767 |TCT|AGA|aga|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg ! |XbaI| ! ! ---FR3----------------------------------------------------| !   17  18  19  20 ! 106 107 108 109 !    N   S   L   s   l   s   i   t   s   q 3806 |aac|agC|TTA|Ag t ctg agc att CGG TCC G !        |AflII|               RsrII.. ! !        g   h   s   p   t   . 3834    gg caa cat tct cca aac tga ccagacga cacaaacggc 3872 ttacgctaaa tcccgcgcat gggatggtaa agaggtggcg tctttgctgg cctggactca 3934 tcagatgaag gccaaaaatt ggcaggagtg gacacagcag gcagcgaaac aagcactgac 3992 catcaactgg tactatgctg atgtaaacgg caatattggt tatgttcata ctggtgctta 4052 tccagatcgt caatcaggcc atgatccgcg attacccgtt cctggtacgg gaaaatggga 4112 ctggaaaggg ctattgcctt ttgaaatgaa ccctaaggtg tataaccccc ag 4164       aa GCTAGC ctgcggcttc !          NheI.. ! 4182 G|GTC|ACC|                                       gtc tca agc ! |BstEII| ! ! 137 137 138 139 140 141 142 143 144 145 146 147 148 149 150 !  A   S   T   K   G   P   S   V   F   P   L   A   P   S   S 4198 gcc tcc acc aag ggc cca tcg gtc ttc ccc ctg gca ccc tcc tcc ! ! 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 !  K   S   T   S   G   G   T   A   A   L   G   C   L   V   K 4243 aag agc acc tct ggg ggc aca gcg gcc ctg ggc tgc ctg gtc aag ! ! 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 !  D   Y   F   P   E   P   V   T   V   S   W   N   S   G   A 4288 gac tac ttc ccc gaa ccg gtg acg gtg tcg tgg aac tca ggc gcc ! ! 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 !  L   T   S   G   V   H   T   F   P   A   V   L   Q   S   S 4333 ctg acc agc ggc gtc cac acc ttc ccg gct gtc cta cag tcc tca ! ! 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !  G   L   Y   S   L   S   S   V   V   T   V   P   S   S   S 4378 gga ctc tac tcc ctc agc agc gta gtg acc gtg ccc tcc agt agc ! ! 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 !  L   G   T   Q   T   Y   I   C   N   V   N   H   K   P   S 4423 ttg ggc acc cag acc tac atc tgc aac gtg aat cac aag ccc agc ! ! 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 !  N   T   K   V   D   K   K   V   E   P   K   S   C 4468 aac acc aag gtg gac aaG AAA GTT GAG CCC AAA TCT TGT !                  CN-TQHCforw...................... ! !                  Poly His linker !          139 140 141 142 143 144 145 146 147 148 149 150 !           A   A   A   H   H   H   H   H   H   G   A   A 4507          GCG GCC GCa cat cat cat cac cat cac ggg gcc gca !          NotI...... !          EagI.... ! ! 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 !  E   Q   K   L   I   S   E   E   D   L   N   G   A   A 4543 gaa caa aaa ctc atc tca gaa gag gat ctg aat ggg gcc gca tag ! ! Mature III--------------------------------------------------... ! 166 167 168 169 170 171 172 173 174 175 176 177 178 178 180 !  T   V   E   S   C   L   A   K   P   H   T   E   N   S   F 4588 act ggt gaa agt tgt tta gca aaa cct cat aca gaa aat tca ttt ! ! 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 !  T   N   V   W   K   D   D   K   T   L   D   R   Y   A   N 4633 act aac gtc tgg aaa gac gac aaa act tta gat cgt tac gct aac ! ! 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 !  Y   E   G   C   L   W   N   A   T   G   V   V   V   C   T 4678 tat gag ggc tgt ctg tgG AAT GCt aca ggc gtt gtg gtt tgt act !                  BsmI.... ! ! 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 !  G   D   E   T   Q   C   Y   G   T   W   V   P   I   G   L 4723 ggt gac gaa act cag tgt tac ggt aca tgg gtt cct att ggg ctt ! ! 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 !  A   I   P   E   N   E   G   G   G   S   E   G   G   G   S 4768 gct atc cct gaa aat gag ggt ggt ggc tct gag ggt ggc ggt tct ! ! 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 !  E   G   G   G   S   E   G   G   G   T   K   P   P   E   Y 4813 gag ggt ggc ggt tct gag ggt ggc ggt act aaa cct cct gag tac ! ! 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 !  G   D   T   P   I   P   G   Y   T   Y   I   N   P   L   D 4858 ggt gat aca cct att ccg ggc tat act tat atc aac cct ctc gac ! ! 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 !  G   T   Y   P   P   G   T   E   Q   N   P   A   N   P   N 4903 ggc act tat ccg cct ggt act gag caa aac ccc gct aat cct aat ! ! 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 !  P   S   L   E   E   S   Q   P   L   N   T   F   M   F   Q 4948 cct tct ctt GAG GAG tct cag cct ctt aat act ttc atg ttt cag !          BseRI..(2 2) ! ! 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 !  N   N   R   F   R   N   R   Q   G   A   L   T   V   Y   T 4993 aat aat agg ttc cga aat agg cag ggt gca tta act gtt tat acg ! ! 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 !  G   T   V   T   Q   G   T   D   P   V   K   T   Y   Y   Q 5038 ggc act gtt act caa ggc act gac ccc gtt aaa act tat tac cag ! ! 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 !  Y   T   P   V   S   S   K   A   M   Y   D   A   Y   W   N 5083 tac act cct gta tca tca aaa gcc atg tat gac gct tac tgg aac ! ! 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 !  G   K   P   R   D   C   A   F   H   S   G   P   N   E   D 5128 ggt aaa ttc aga gac tgc gct ttc cat tct ggc ttt aat gaG GAT !                                           BamHI.. ! ! 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 !  P   F   V   C   E   Y   Q   G   Q   S   S   D   L   P   Q 5173 CCa ttc gtt tgt gaa tat caa ggc caa tcg tct gAC CTG Cct caa ! BAMHI...                                  BspMI...(2 2) ! ! 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 !  P   P   V   N   A   G   G   G   S   G   G   G   S   G   G 5218 cct cct gtc aat gct ggc ggc ggc tct ggt ggt ggt tct ggt ggc ! ! 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 !  G   S   E   G   G   G   S   E   G   G   G   S   E   G   G 5263 ggc tct gag ggt ggc ggc tct gag ggt ggc ggt tct gag ggt ggc ! ! 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 !  G   S   E   G   G   G   S   G   G   G   S   G   S   G   D 5308 ggc tct gag ggt ggc ggt tcc ggt ggc ggc tcc ggt tcc ggt gat ! ! 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 !  F   D   Y   E   K   M   A   N   A   N   K   G    A   M   T 5353 ttt gat tat gaa aaa atg gca aac gct aat aag ggg gct atg acc ! ! 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 !  E   N   A   D   E   N   A   L   Q   S   D   A   K   G   K 5398 gaa aat gcc gat gaa aac gcg cta cag tct gac gct aaa ggc aaa ! ! 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 !  L   D   S   V   A   T   D   Y   G   A   A   I   D   G   F 5443 ctt gat tct gtc gct act gat tac ggt gct gct ATC GAT ggt ttc !                                  BspDI.. ! ! 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 !  I   G   D   V   S   G   L   A   N   G   N   G   A   T   G 5488 att ggt gac gtt tcc ggc ctt gct aat ggt aat ggt gct act ggt ! ! 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 !  D   F   A   G   S   N   S   Q   M   A   Q   V   G   D   G 5533 gat ttt gct ggc tct aat tcc caa atg gct caa gtc ggt gac ggt ! ! 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 !  D   N   S   P   L   M   N   N   F   R   Q   Y   L   P   S 5578 gat aat tca cct tta atg aat aat ttc cgt caa tat tta cct tct ! ! 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 !  L   P   Q   S   V   E   C   R   P   Y   V   F   G   A   G 5623 ttg cct cag tcg gtt gaa tgt cgc cct tat gtc ttt ggc gct ggt ! ! 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 !  K   P   Y   E   P   S   I   D   C   D   K   I   N   L   F 5668 aaa cCA TAT Gaa ttt tct att gat tgt gac aaa ata aac tta ttc !     NdeI ! ! 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 !  R   G   V   F   A   F   L   L   Y   V   A   T   F   M   Y 5713 cgt ggt gtc ttt gcg ttt ctt tta tat gtt gcc acc ttt atg tat ! ! 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 !  V   F   S   T   F   A   N   I   L   R   N   K   E   S   . 5758 gta ttt tcg acg ttt gct aac ata ctg cgt aat aag gag tct taa ! ! 571 !  . 5803 taa GAATTC !    EcoRI. 5812 actggccgt cgttttacaa cgtcgtgact gggaaaaccc tggcgttacc caacttaatc 5871 gccttgcagc acatccccct ttcgccagct ggcgtaatag cgaagaggcc cgcacCGATC ! 5931 Gcccttccca acagtTGCGC Agcctgaatg gcgaatGGCG CCtgatgcgg tattttctcc !...PvuI... (3 3)                FspI... (2 2)          KasI...(2 2) 5991 ttacgcatct gtgcggtatt tcacaccgca tataaattgt aaacgttaat attttgttaa 6051 aattcgcgtt aaatttttgt taaatcagct cattttttaa ccaataggcc gaaatcggca 6111 aaatcccTTA TAAatcaaaa gaatagcccg agatagggtt gagtgttgtt ccagtttgga !        PsiI... 6171 acaagagtcc actattaaag aacgtggact ccaacgtcaa agggcgaaaa accgtctatc 6231 agggcgatgg ccCACtacGT Gaaccatcac ccaaatcaag ttttttgggg tcgaggtgcc !             DraIII.... 6291 gtaaagcact aaatcggaac cctaaaggga gcccccgatt tagagcttga cggggaaaGC !                                                           NgoMIV.. 6351 CGGCgaacgt ggcgagaaag gaagggaaga aagcgaaagg agcgggcgct agggcgctgg !..NGoMIV.(2 2) 6411 caagtgtagc ggtcacgctg cgcgtaacca ccacacccgc cgcgcttaat gcgccgctac 6471 agggcgcgta ctatggttgc tttgacgggt gcagtctcag tacaatctgc tctgatgccg 6531 catagttaag ccagccccga cacccgccaa cacccgctga cgcgccctga cgggcttgtc 6591 tgctcccggc atccgcttac agacaagctg tgaccgtctc cgggagctgc atgtgtcaga 6651 ggttttcacc gtcatcaccg aaacgcgcga

[0179] TABLE 630 Oligonucleotides used to clone CDR1/2 diversity All sequences are 5′ to 3′. 1) on_CD1Bsp, 30 bases A c c T c A c T g g c T T c c g g A 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 T T c A c T T T c T c T 19 20 21 22 23 24 25 26 27 28 29 30 2) ON_Br12, 42 bases A g A A A c c c A c T c c A A A c c 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 T T T A c c A g g A g c T T g g c g 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 A A c c c A 37 38 39 40 41 42 3) ON_CD2Xba, 51 bases g g A A g g c A g T g A T c T A g A 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 g A T A g T g A A g c g A c c T T T 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 A A c g g A g T c A g c A T A 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 4) ON_BotXba, 23 bases g g A A g g c A g T g A T c T A g A 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 g A T A g 19 20 21 22 23 

We claim:
 1. A method for cleaving single-stranded nucleic acid sequences at a desired location, the method comprising the steps of: (i) contacting the nucleic acid with a single-stranded oligonucleotide, the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired and including a sequence that with its complement in the nucleic acid forms a restriction endonuclease recognition site that on restriction results in cleavage of the nucleic acid at the desired location; and (ii) cleaving the nucleic acid solely at the recognition site formed by the complementation of the nucleic acid and the oligonucleotide; the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.
 2. A method for cleaving single-stranded nucleic acid sequences at a desired location, the method comprising the steps of: (i) contacting the nucleic acid with a partially double-stranded oligonucleotide, the single-stranded region of the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired, and the double-stranded region of the oligonucleotide having a Type II-S restriction endonuclease recognition site, whose cleavage site is located at a known distance from the recognition site; and (ii) cleaving the nucleic acid solely at the Type 11-S cleavage site formed by the complementation of the nucleic acid and the single-stranded region of the oligonucleotide; the contacting and the cleaving steps being performed a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.
 3. In a method for displaying a member of a diverse family of peptides, polypeptides or proteins on the surface of a genetic package and collectively displaying at least a part of the diversity of the family, the improvement being characterized in that the displayed at least a part of peptide, polypeptide or protein is encoded at least in part by a nucleic acid that has been cleaved at a desired location by a method comprising the steps of: (i) contacting the nucleic acid with a single-stranded oligonucleotide, the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired and including a sequence that with its complement in the nucleic acid forms a restriction endonuclease recognition site that on restriction results in cleavage of the nucleic acid at the desired location; and (ii) cleaving the nucleic acid solely at the recognition site formed by the complementation of the nucleic acid and the oligonucleotide; the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.
 4. In a method for displaying a member of a diverse family of peptides, polypeptides or proteins on the surface of a genetic package and collectively displaying at least a part of the diversity of the family, the improvement being characterized in that the displayed peptide, polypeptide or protein is encoded by a DNA sequence comprising a nucleic acid that has been cleaved at a desired location by (i) contacting the nucleic acid with a partially double-stranded oligonucleotide, the single-stranded region of the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired, and the double-stranded region of the oligonucleotide having a Type II-S restriction endonuclease recognition site, whose cleavage site is located at a known distance from the recognition site; and (ii) cleaving the nucleic acid solely at the Type II-S cleavage site formed by the complementation of the nucleic acid and the single-stranded region of the oligonucleotide; the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desires location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.
 5. A method for displaying a member of a diverse family of peptides, polypeptides or proteins on the surface of a genetic package and collectively displaying at least a part of the diversity of the family, the method comprising the steps of: (i) preparing a collection of nucleic acids that code at least in part for members of the diverse family; (ii) rendering the nucleic acids single-stranded; (iii) cleaving the single-stranded nucleic acids at a desired location by a method comprising the steps of: (a) contacting the nucleic acid with a single-stranded oligonucleotide, the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired and including a sequence that with its complement in the nucleic acid forms a restriction endonuclease recognition site that on restriction results in cleavage of the nucleic acid at the desired location; and (b) cleaving the nucleic acid solely at the recognition site formed by the complementation of the nucleic acid and the oligonucleotide;  the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature; and (iv) displaying a member of the family of peptides, polypeptides or proteins coded, at least in part, by the cleaved nucleic acids on the surface of the genetic package and collectively displaying at least a portion of the diversity of the family.
 6. A method for displaying a member of a diverse family of peptides, polypeptides or proteins on the surface of a genetic package and collectively displaying at least a portion of the diversity of the family, the method comprising the steps of: (i) preparing a collection of nucleic acids that code, at least in part, for members of the diverse family; (ii) rendering the nucleic acids single-stranded; (iii) cleaving the single-stranded nucleic acids at a desired location by a method comprising the steps of: (a) contacting the nucleic acid with a partially double-stranded oligonucleotide, the single-stranded region of the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired, and the double-stranded region of the oligonucleotide having a Type II-S restriction endonuclease recognition site, whose cleavage site is located at a known distance from the recognition site; and (b) cleaving the nucleic acid solely at the Type II-S cleavage site formed by the complementation of the nucleic acid and the single-stranded region of the oligonucleotide;  the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the restriction being carried out using a cleavage endonuclease that is active at the chosen temperature; and (iv) displaying a member of the family of peptides, polypeptides or proteins coded, at least in part, by the cleaved nucleic acids on the surface of the genetic package and collectively displaying at least a portion of the diversity of the family.
 7. A library comprising a collection of genetic packages that display a member of a diverse family of peptides, polypeptides or proteins and collectively display at least a portion of the diversity of the family, the library being produced using the methods of claims 3, 4, 5 or
 6. 8. A library comprising a collection of genetic packages that display a member of a diverse family of peptides, polypeptides or proteins and that collectively display at least a portion of the family, the displayed peptides, polypeptides or proteins being encoded by DNA sequences comprising at least in part sequences produced by cleaving single-stranded nucleic acid sequences at a desired location by a method comprising the steps of: (i) contacting the nucleic acid with a single-stranded oligonucleotide, the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired and including a sequence that with its complement in the nucleic acid forms a restriction endonuclease recognition site that on restriction results in cleavage of the nucleic acid at the desired location; and (ii) cleaving the nucleic acid solely at the recognition site formed by the complementation of the nucleic acid and the oligonucleotide; the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.
 9. A library comprising a collection of genetic packages that display a member of a diverse family of peptides, polypeptides or proteins and that collectively display at least a portion of the diversity of the family of the displayed peptides, polypeptides or proteins being encoded by DNA sequences comprising at least in part sequences produced by cleaving single-stranded nucleic acid sequences at a desired location by a method comprising the steps of: (i) contacting the nucleic acid with a partially double-stranded oligonucleotide, the single-stranded region of the oligonucleotide being functionally complementary to the nucleic acid in the region in which cleavage is desired, and the double-stranded region of the oligonucleotide having a Type II S restriction endonuclease recognition site, whose cleavage site is located at a known distance from the recognition site where the cleavage of the nucleic acid is desired; and (ii) cleaving the nucleic acid solely at the Type II-S cleavage site formed by the complementation of the nucleic acid and the single-stranded region of the oligonucleotide; the contacting and the cleaving steps being performed at a temperature sufficient to maintain the nucleic acid in substantially single-stranded form, the oligonucleotide being functionally complementary to the nucleic acid over a large enough region to allow the two strands to associate such that cleavage may occur at the chosen temperature and at the desired location, and the cleavage being carried out using a restriction endonuclease that is active at the chosen temperature.
 10. The methods according to any one of claims 1 to 9, wherein the nucleic acids encode at least a portion of an immunoglobulin.
 11. The methods according to claim 10, wherein the immunoglobulin comprises a Fab or single chain Fv.
 12. The methods according to claim 10 or 11, wherein the immunoglobin comprises at least portion of a heavy chain.
 13. The methods according to claim 12, wherein at least a portion of the heavy chain is human.
 14. The methods according to claim 10 or 11, wherein the immunoglobulin comprises at least a portion of FR1.
 15. The methods according to claim 14, wherein at least a portion of the FR1 is human.
 16. The methods according to claim 10 or 11, wherein the immunoglobulin comprises at least a portion of a light chain.
 17. The methods according to claim 16, wherein at least a portion of the light chain is human.
 18. The methods according to any one of claims 1 to 9, wherein the nucleic acid sequences are at least in part derived from patients suffering from at least one autoimmune disease and/or cancer.
 19. The methods according to claim 18, wherein the autoimmune disease is selected from the group comprising lupus, erythematosus, systemic sclerosis, rheumatoid arthritis, antiphosolipid syndrome or vasculitis.
 20. The methods according to claim 18, wherein the nucleic acids are at least in part isolated from the group comprising peripheral blood cells, bone marrow cells spleen cells or lymph node cells.
 21. The methods according to claim 5 or 6 further comprising an nucleic acid amplification step between steps (i) and (ii), between steps (ii) and (iii) or between steps (iii) and (iv).
 22. The methods according to claim 21, wherein the amplification step uses geneRACE™.
 23. The methods according to any one of claims 1 to 9, wherein the temperature is between 45° C. and 75° C.
 24. The methods according to claim 23, wherein the temperature is between 50° C. and 60° C.
 25. The methods according to claim 24, wherein the temperature is between 55° C. and 60° C.
 26. The methods according to claim 1, 3, 5 or 8, wherein the length of the single-stranded oligonucleotide is between 17 and 30 bases.
 27. The methods according to claim 26, wherein the length of the single-stranded oligonucleotide is between 18 and 24 bases.
 28. The methods according to claim 1, 3, 5 or 8, wherein the restriction endonuclease is selected from the group comprising MaelII, Tsp45I, HphI, BsaJI, AluI, BlpI, DdeI, BglII, MslI, BsiEI, EaeI, EagI, HaeIII, Bst4CI, HpyCH41II, HinfI, MlyI, PleI, MnlI, HpyCH4V, BsmAI, BpmI, XmnI, or SacI.
 29. The methods according to claim 28, wherein the restriction endonuclease is selected from the group comprising Bst4CI, TaaI, HpyCH4III, BlpI, HpyCH4V or MslI.
 30. The methods according to claim 2, 4, 6 or 9, wherein the length of the single-stranded region of the partially double-stranded oligonucleotide is between 14 and 22 bases.
 31. The methods according to claim 30, wherein the length of the single-stranded region of the partially double-stranded oligonucleotide is between 14 and 17 bases.
 32. The methods according to claim 31, wherein the length of the single-stranded region of the oligonucleotide is between 18 and 20 bases.
 33. The methods according to claim 2, 4, 6 or 9, wherein the length of the double-stranded region of the partially double-stranded oligonucleotide is between 10 and 14 base pairs formed by a stem and its palindrome.
 34. The methods according to claim 33 wherein, the partially double-stranded oligonucleotide comprises a loop of 3 to 8 bases between the stem and the palindrome.
 35. The methods according to claim 2, 4, 6 or 9, wherein the Type II-S restriction endonuclease is selected from the group comprising AarICAC, AceIII, Bbr7I, BbvI, BbvII, Bce83I, BceAI, BcefI, BciVI, BfiI, BinI, BscAI, BseRI, BsmFI, BspMI, EciI, Eco57I, FauI, FokI, GsuI, HgaI, HphI, MboII, MlyI, MmeI, MnlI, PleI, RleAI, SfaNI, SspD5I, Sthl32I, StsI, TaqII, Tth111II, or UbaPI.
 36. The methods according to claim 35, wherein the Type II-S restriction endonuclease is FokI.
 37. A method for preparing single-stranded nucleic acids for cloning into an vector, the method comprising the steps of: (i) contacting a single-stranded nucleic acid sequence that has been cleaved with a restriction endonuclease with a partially double-stranded oligonucleotide, the single-stranded region of the oligonucleotide being functionally complementary to the nucleic acid in the region that remains after cleavage, the double-stranded region of the oligonucleotide including any sequences necessary to return the sequences that remain after cleavage into proper and original reading frame for expression and containing a restriction endonuclease recognition site 5′ of those sequences; and (ii) cleaving the partially double-stranded oligonucleotide sequence solely at the restriction endonuclease recognition site contained within the double-stranded region of the partially double-stranded oligonucleotide.
 38. The method according to claim 37, wherein the length of the single-stranded portion of the partially double-stranded oligonucleotide is between 2 and 15 bases.
 39. The method according to claim 38, wherein the length of the single-stranded portion of the partially double-stranded oligonucleotide is between 7 and 10 bases.
 40. The method according to claim 37, wherein the length of the double-stranded portion of the partially double-stranded oligonucleotide is between 12 and 100 base pairs.
 41. The method according to claim 40, wherein the length of the double-stranded portion of the partially double-stranded oligonucleotide is between 20 and 100 base pairs. 